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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:logitT.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings logitT_1.60.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/logitT.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘logitT/DESCRIPTION’ ... OK
* this is package ‘logitT’ version ‘1.60.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘logitT’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'logitT' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.18-bioc/meat/logitT.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘affy’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘affy’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
logitTAffy: no visible global function definition for ‘featureNames’
logitTAffy: no visible global function definition for ‘pm’
logitTAffy: no visible global function definition for ‘mm’
logitTAffy: no visible global function definition for ‘pmindex’
Undefined global functions or variables:
  featureNames mm pm pmindex
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.18-bioc/R/site-library/logitT/libs/logitT.so’:
  Found ‘stdout’, possibly from ‘stdout’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘logitT-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: logitTAffy
> ### Title: Testing for differential gene expression using the Logit-t
> ###   algorithm
> ### Aliases: logitTAffy
> 
> ### ** Examples
> 
> if(require(SpikeInSubset)){
+ library(SpikeInSubset)
+ data(spikein95)
+ logitTex<-logitTAffy(spikein95, group=c("A","A","A","B","B","B"))
+ logitTex[1:10]                                                              # extract t-statistics for first ten probe sets
+ logitTex[grep("AFFX-BioB-5_at",names(logitTex))]                         # extract t-statistics for specific probe set
+ pvals<-(1-pt(abs(logitTex),df=4))*2                                         # calculate two-sided p-values
+ signifgenes<-names(logitTex)[pvals<0.01]                                    # find significant probe sets at 0.01 significance level
+ }else{
+ stop("Please install the SpikeInSubset package to run the example.")
+ }
Loading required package: SpikeInSubset
     [,1] [,2]
[1,]    1    3
[2,]    2    3
Extracting max and min probe data...
also installing the dependencies ‘sys’, ‘bitops’, ‘cli’, ‘glue’, ‘lifecycle’, ‘fastmap’, ‘askpass’, ‘RCurl’, ‘GenomeInfoDbData’, ‘bit’, ‘vctrs’, ‘cachem’, ‘curl’, ‘jsonlite’, ‘mime’, ‘openssl’, ‘R6’, ‘XVector’, ‘GenomeInfoDb’, ‘crayon’, ‘bit64’, ‘blob’, ‘memoise’, ‘pkgconfig’, ‘rlang’, ‘httr’, ‘png’, ‘Biostrings’, ‘IRanges’, ‘DBI’, ‘RSQLite’, ‘S4Vectors’, ‘KEGGREST’, ‘AnnotationDbi’

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* installing *source* package ‘sys’ ...
** package ‘sys’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c exec.c -o exec.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o sys.so exec.o init.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /tmp/RtmphifQjq/RLIBS_33fecac109801/00LOCK-sys/00new/sys/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (sys)
* installing *source* package ‘bitops’ ...
** package ‘bitops’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c bit-ops.c -o bit-ops.o
bit-ops.c: In function ‘bitShiftL’:
bit-ops.c:125:80: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses]
  125 |                 else *(xaAb++)=(double) (_2_UINT_(xa[i]) __OP__ I_2_UINT(xb[j] & 31 ) ) ; \
      |                                                                                ^
bit-ops.c:6:50: note: in definition of macro ‘I_2_UINT’
    6 | #define I_2_UINT(I)   (unsigned int) ((I) < 0 ? (I + UINT_MAX +1) : (I))
      |                                                  ^
bit-ops.c:145:5: note: in expansion of macro ‘bitshift_BODY’
  145 |     bitshift_BODY( << );
      |     ^~~~~~~~~~~~~
bit-ops.c:136:80: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses]
  136 |                 else *(xaAb++)=(double) (_2_UINT_(xa[j]) __OP__ I_2_UINT(xb[i] & 31 )) ; \
      |                                                                                ^
bit-ops.c:6:50: note: in definition of macro ‘I_2_UINT’
    6 | #define I_2_UINT(I)   (unsigned int) ((I) < 0 ? (I + UINT_MAX +1) : (I))
      |                                                  ^
bit-ops.c:145:5: note: in expansion of macro ‘bitshift_BODY’
  145 |     bitshift_BODY( << );
      |     ^~~~~~~~~~~~~
bit-ops.c: In function ‘bitShiftR’:
bit-ops.c:125:80: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses]
  125 |                 else *(xaAb++)=(double) (_2_UINT_(xa[i]) __OP__ I_2_UINT(xb[j] & 31 ) ) ; \
      |                                                                                ^
bit-ops.c:6:50: note: in definition of macro ‘I_2_UINT’
    6 | #define I_2_UINT(I)   (unsigned int) ((I) < 0 ? (I + UINT_MAX +1) : (I))
      |                                                  ^
bit-ops.c:149:5: note: in expansion of macro ‘bitshift_BODY’
  149 |     bitshift_BODY( >> );
      |     ^~~~~~~~~~~~~
bit-ops.c:136:80: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses]
  136 |                 else *(xaAb++)=(double) (_2_UINT_(xa[j]) __OP__ I_2_UINT(xb[i] & 31 )) ; \
      |                                                                                ^
bit-ops.c:6:50: note: in definition of macro ‘I_2_UINT’
    6 | #define I_2_UINT(I)   (unsigned int) ((I) < 0 ? (I + UINT_MAX +1) : (I))
      |                                                  ^
bit-ops.c:149:5: note: in expansion of macro ‘bitshift_BODY’
  149 |     bitshift_BODY( >> );
      |     ^~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c cksum.c -o cksum.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o bitops.so bit-ops.o cksum.o init.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /tmp/RtmphifQjq/RLIBS_33fecac109801/00LOCK-bitops/00new/bitops/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (bitops)
* installing *source* package ‘cli’ ...
** package ‘cli’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c ansi.c -o ansi.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c cleancall.c -o cleancall.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c diff.c -o diff.o
diff.c: In function ‘clic_diff_chr’:
diff.c:104:3: warning: ‘sn’ may be used uninitialized [-Wmaybe-uninitialized]
  104 |   SET_VECTOR_ELT(result, 0, allocVector(INTSXP, sn));
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c errors.c -o errors.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c glue.c -o glue.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c inst.c -o inst.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c keypress-unix.c -o keypress-unix.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c keypress-win.c -o keypress-win.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c keypress.c -o keypress.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c md5.c -o md5.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c progress-altrep.c -o progress-altrep.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c progress.c -o progress.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c sha1.c -o sha1.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c sha256.c -o sha256.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c thread.c -o thread.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c tty.c -o tty.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c utf8.c -o utf8.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c utils.c -o utils.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c vt.c -o vt.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c vtparse.c -o vtparse.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c vtparse_table.c -o vtparse_table.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c win-utf8.c -o win-utf8.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c winfiles.c -o winfiles.o
gcc -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o cli.so ansi.o cleancall.o diff.o errors.o glue.o init.o inst.o keypress-unix.o keypress-win.o keypress.o md5.o progress-altrep.o progress.o sha1.o sha256.o thread.o tty.o utf8.o utils.o vt.o vtparse.o vtparse_table.o win-utf8.o winfiles.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /tmp/RtmphifQjq/RLIBS_33fecac109801/00LOCK-cli/00new/cli/libs
** R
** exec
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (cli)
* installing *source* package ‘glue’ ...
** package ‘glue’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c glue.c -o glue.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c trim.c -o trim.o
gcc -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o glue.so glue.o init.o trim.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /tmp/RtmphifQjq/RLIBS_33fecac109801/00LOCK-glue/00new/glue/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (glue)
* installing *source* package ‘fastmap’ ...
** package ‘fastmap’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Ilib/  -I/usr/local/include   -DR_NO_REMAP -fpic  -g -O2  -Wall -c fastmap.cpp -o fastmap.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Ilib/  -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o fastmap.so fastmap.o init.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /tmp/RtmphifQjq/RLIBS_33fecac109801/00LOCK-fastmap/00new/fastmap/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (fastmap)
* installing *source* package ‘GenomeInfoDbData’ ...
** using staged installation
** data
** inst
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GenomeInfoDbData)
* installing *source* package ‘bit’ ...
** package ‘bit’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c attrutil.c -o attrutil.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c bit.c -o bit.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c chunkutil.c -o chunkutil.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c clone.c -o clone.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c integerutil.c -o integerutil.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c merge.c -o merge.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c rle.c -o rle.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c sort.c -o sort.o
gcc -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o bit.so attrutil.o bit.o chunkutil.o clone.o init.o integerutil.o merge.o rle.o sort.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /tmp/RtmphifQjq/RLIBS_33fecac109801/00LOCK-bit/00new/bit/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (bit)
* installing *source* package ‘curl’ ...
** package ‘curl’ successfully unpacked and MD5 sums checked
** using staged installation
Found pkg-config cflags and libs!
Using PKG_CFLAGS=-I/usr/include/x86_64-linux-gnu
Using PKG_LIBS=-lcurl
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
rm -f curl.so callbacks.o curl.o download.o escape.o fetch.o findport.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o options.o reflist.o split.o ssl.o typechecking.o utils.o version.o winidn.o writer.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c callbacks.c -o callbacks.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c curl.c -o curl.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c download.c -o download.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c escape.c -o escape.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c fetch.c -o fetch.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c findport.c -o findport.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c form.c -o form.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c getdate.c -o getdate.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c handle.c -o handle.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c ieproxy.c -o ieproxy.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c interrupt.c -o interrupt.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c multi.c -o multi.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c nslookup.c -o nslookup.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c options.c -o options.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c reflist.c -o reflist.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c split.c -o split.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c ssl.c -o ssl.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c typechecking.c -o typechecking.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c utils.c -o utils.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c version.c -o version.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c winidn.c -o winidn.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c writer.c -o writer.o
gcc -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o curl.so callbacks.o curl.o download.o escape.o fetch.o findport.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o options.o reflist.o split.o ssl.o typechecking.o utils.o version.o winidn.o writer.o -lcurl -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /tmp/RtmphifQjq/RLIBS_33fecac109801/00LOCK-curl/00new/curl/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (curl)
* installing *source* package ‘jsonlite’ ...
** package ‘jsonlite’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c base64.c -o base64.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c collapse_array.c -o collapse_array.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c collapse_object.c -o collapse_object.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c collapse_pretty.c -o collapse_pretty.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c escape_chars.c -o escape_chars.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c integer64_to_na.c -o integer64_to_na.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c is_datelist.c -o is_datelist.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c is_recordlist.c -o is_recordlist.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c is_scalarlist.c -o is_scalarlist.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c modp_numtoa.c -o modp_numtoa.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c null_to_na.c -o null_to_na.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c num_to_char.c -o num_to_char.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c parse.c -o parse.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c prettify.c -o prettify.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c push_parser.c -o push_parser.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c r-base64.c -o r-base64.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c register.c -o register.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c row_collapse.c -o row_collapse.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c transpose_list.c -o transpose_list.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c validate.c -o validate.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c yajl/yajl.c -o yajl/yajl.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c yajl/yajl_alloc.c -o yajl/yajl_alloc.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c yajl/yajl_buf.c -o yajl/yajl_buf.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c yajl/yajl_encode.c -o yajl/yajl_encode.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c yajl/yajl_gen.c -o yajl/yajl_gen.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c yajl/yajl_lex.c -o yajl/yajl_lex.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c yajl/yajl_parser.c -o yajl/yajl_parser.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c yajl/yajl_tree.c -o yajl/yajl_tree.o
ar rcs yajl/libstatyajl.a yajl/yajl.o yajl/yajl_alloc.o yajl/yajl_buf.o yajl/yajl_encode.o yajl/yajl_gen.o yajl/yajl_lex.o yajl/yajl_parser.o yajl/yajl_tree.o
gcc -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o jsonlite.so base64.o collapse_array.o collapse_object.o collapse_pretty.o escape_chars.o integer64_to_na.o is_datelist.o is_recordlist.o is_scalarlist.o modp_numtoa.o null_to_na.o num_to_char.o parse.o prettify.o push_parser.o r-base64.o register.o row_collapse.o transpose_list.o validate.o -Lyajl -lstatyajl -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /tmp/RtmphifQjq/RLIBS_33fecac109801/00LOCK-jsonlite/00new/jsonlite/libs
** R
** inst
** byte-compile and prepare package for lazy loading
in method for ‘asJSON’ with signature ‘"AsIs"’: no definition for class “AsIs”
in method for ‘asJSON’ with signature ‘"ITime"’: no definition for class “ITime”
in method for ‘asJSON’ with signature ‘"hms"’: no definition for class “hms”
in method for ‘asJSON’ with signature ‘"json"’: no definition for class “json”
in method for ‘asJSON’ with signature ‘"integer64"’: no definition for class “integer64”
in method for ‘asJSON’ with signature ‘"pairlist"’: no definition for class “pairlist”
in method for ‘asJSON’ with signature ‘"blob"’: no definition for class “blob”
in method for ‘asJSON’ with signature ‘"scalar"’: no definition for class “scalar”
in method for ‘asJSON’ with signature ‘"sf"’: no definition for class “sf”
in method for ‘asJSON’ with signature ‘"sfc"’: no definition for class “sfc”
in method for ‘asJSON’ with signature ‘"vctrs_vctr"’: no definition for class “vctrs_vctr”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (jsonlite)
* installing *source* package ‘mime’ ...
** package ‘mime’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c rawmatch.c -o rawmatch.o
gcc -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o mime.so init.o rawmatch.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /tmp/RtmphifQjq/RLIBS_33fecac109801/00LOCK-mime/00new/mime/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (mime)
* installing *source* package ‘R6’ ...
** package ‘R6’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (R6)
* installing *source* package ‘crayon’ ...
** package ‘crayon’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (crayon)
* installing *source* package ‘pkgconfig’ ...
** package ‘pkgconfig’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (pkgconfig)
* installing *source* package ‘rlang’ ...
** package ‘rlang’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang/  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c capture.c -o capture.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang/  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c internal.c -o internal.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang/  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c rlang.c -o rlang.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang/  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c version.c -o version.o
gcc -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o rlang.so capture.o internal.o rlang.o version.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /tmp/RtmphifQjq/RLIBS_33fecac109801/00LOCK-rlang/00new/rlang/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rlang)
* installing *source* package ‘png’ ...
** package ‘png’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    `libpng-config --cflags` -fpic  -g -O2  -Wall -c dummy.c -o dummy.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    `libpng-config --cflags` -fpic  -g -O2  -Wall -c read.c -o read.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    `libpng-config --cflags` -fpic  -g -O2  -Wall -c write.c -o write.o
gcc -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o png.so dummy.o read.o write.o -lpng16 -lm -lz -lm -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /tmp/RtmphifQjq/RLIBS_33fecac109801/00LOCK-png/00new/png/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (png)
* installing *source* package ‘DBI’ ...
** package ‘DBI’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DBI)
* installing *source* package ‘S4Vectors’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c AEbufs.c -o AEbufs.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c DataFrame_class.c -o DataFrame_class.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c Hits_class.c -o Hits_class.o
In file included from /home/biocbuild/bbs-3.18-bioc/R/include/Rdefines.h:41,
                 from ../inst/include/S4Vectors_defines.h:18,
                 from S4Vectors.h:1,
                 from Hits_class.c:4:
Hits_class.c: In function ‘Hits_new’:
/home/biocbuild/bbs-3.18-bioc/R/include/Rinternals.h:886:33: warning: ‘revmap’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  886 | #define defineVar               Rf_defineVar
      |                                 ^~~~~~~~~~~~
Hits_class.c:216:19: note: ‘revmap’ was declared here
  216 |         SEXP ans, revmap, symbol;
      |                   ^~~~~~
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c LLint_class.c -o LLint_class.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c List_class.c -o List_class.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c R_init_S4Vectors.c -o R_init_S4Vectors.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c Rle_class.c -o Rle_class.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c Rle_utils.c -o Rle_utils.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c SEXP_utils.c -o SEXP_utils.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c SimpleList_class.c -o SimpleList_class.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c anyMissing.c -o anyMissing.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c character_utils.c -o character_utils.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c eval_utils.c -o eval_utils.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c hash_utils.c -o hash_utils.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c integer_utils.c -o integer_utils.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c logical_utils.c -o logical_utils.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c map_ranges_to_runs.c -o map_ranges_to_runs.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c raw_utils.c -o raw_utils.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c safe_arithm.c -o safe_arithm.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c sort_utils.c -o sort_utils.o
sort_utils.c:263:13: warning: ‘sort_uchar_array’ defined but not used [-Wunused-function]
  263 | static void sort_uchar_array(unsigned char *x, int nelt, int desc)
      |             ^~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c subsetting_utils.c -o subsetting_utils.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c vector_utils.c -o vector_utils.o
gcc -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o S4Vectors.so AEbufs.o DataFrame_class.o Hits_class.o LLint_class.o List_class.o R_init_S4Vectors.o Rle_class.o Rle_utils.o SEXP_utils.o SimpleList_class.o anyMissing.o character_utils.o eval_utils.o hash_utils.o integer_utils.o logical_utils.o map_ranges_to_runs.o raw_utils.o safe_arithm.o sort_utils.o subsetting_utils.o vector_utils.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /tmp/RtmphifQjq/RLIBS_33fecac109801/00LOCK-S4Vectors/00new/S4Vectors/libs
** R
** inst
** byte-compile and prepare package for lazy loading
in method for ‘normalizeSingleBracketReplacementValue’ with signature ‘"List"’: no definition for class “List”
Creating a new generic function for ‘unname’ in package ‘S4Vectors’
Creating a new generic function for ‘expand.grid’ in package ‘S4Vectors’
Creating a new generic function for ‘findMatches’ in package ‘S4Vectors’
Creating a generic function for ‘setequal’ from package ‘base’ in package ‘S4Vectors’
in method for ‘coerce’ with signature ‘"Hits","DFrame"’: no definition for class “DFrame”
Creating a generic function for ‘as.factor’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘tabulate’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘cov’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘cor’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘substr’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘substring’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘chartr’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘tolower’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘toupper’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘sub’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘gsub’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘nlevels’ from package ‘base’ in package ‘S4Vectors’
in method for ‘coerce’ with signature ‘"data.table","DFrame"’: no definition for class “data.table”
Creating a generic function for ‘complete.cases’ from package ‘stats’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (S4Vectors)
* installing *source* package ‘lifecycle’ ...
** package ‘lifecycle’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (lifecycle)
* installing *source* package ‘askpass’ ...
** package ‘askpass’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c askpass.c -o askpass.o
gcc -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o askpass.so askpass.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /tmp/RtmphifQjq/RLIBS_33fecac109801/00LOCK-askpass/00new/askpass/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (askpass)
* installing *source* package ‘RCurl’ ...
** package ‘RCurl’ successfully unpacked and MD5 sums checked
** using staged installation
checking for curl-config... /usr/bin/curl-config
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking how to run the C preprocessor... gcc -E
Version has a libidn field
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Version has CURLINFO_SIZE_DOWNLOAD
Version has CURLINFO_SPEED_DOWNLOAD
Version has CURLINFO_SPEED_UPLOAD
Version has CURLINFO_HEADER_SIZE
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Version has CURLINFO_SSL_VERIFYRESULT
Version has CURLINFO_FILETIME
Version has CURLINFO_CONTENT_LENGTH_DOWNLOAD
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Version has CURLOPT_OPENSOCKETFUNCTION
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Version has CURLOPT_COPYPOSTFIELDS
Version has CURLOPT_PROXY_TRANSFER_MODE
Version has CURLOPT_SEEKFUNCTION
Version has CURLOPT_SEEKDATA
Version has CURLOPT_CRLFILE
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Version has CURLOPT_ADDRESS_SCOPE
Version has CURLOPT_CERTINFO
Version has CURLOPT_USERNAME
Version has CURLOPT_PASSWORD
Version has CURLOPT_PROXYUSERNAME
Version has CURLOPT_PROXYPASSWORD
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Version has CURLOPT_NOPROXY
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Version has CURLOPT_LOCALPORTRANGE
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Version has CURLOPT_FTP_ALTERNATIVE_TO_USER
Version has CURLOPT_SOCKOPTFUNCTION
Version has CURLOPT_SOCKOPTDATA
Version has CURLOPT_SSL_SESSIONID_CACHE
libcurl version: libcurl 7.81.0
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include    -fpic  -g -O2  -Wall -c base64.c -o base64.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include    -fpic  -g -O2  -Wall -c curl.c -o curl.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include    -fpic  -g -O2  -Wall -c curlInit.c -o curlInit.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include    -fpic  -g -O2  -Wall -c curl_base64.c -o curl_base64.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include    -fpic  -g -O2  -Wall -c enums.c -o enums.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include    -fpic  -g -O2  -Wall -c json.c -o json.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include    -fpic  -g -O2  -Wall -c memoryManagement.c -o memoryManagement.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include    -fpic  -g -O2  -Wall -c myUTF8.c -o myUTF8.o
gcc -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o RCurl.so base64.o curl.o curlInit.o curl_base64.o enums.o json.o memoryManagement.o myUTF8.o -lcurl -lxml2 -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /tmp/RtmphifQjq/RLIBS_33fecac109801/00LOCK-RCurl/00new/RCurl/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RCurl)
* installing *source* package ‘cachem’ ...
** package ‘cachem’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c cache.c -o cache.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o cachem.so cache.o init.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /tmp/RtmphifQjq/RLIBS_33fecac109801/00LOCK-cachem/00new/cachem/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (cachem)
* installing *source* package ‘bit64’ ...
** package ‘bit64’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c bsearch.c -o bsearch.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c cache.c -o cache.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c hash64.c -o hash64.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c integer64.c -o integer64.o
integer64.c: In function ‘runif_integer64’:
integer64.c:998:15: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  998 |     while( (*((long long *) &ii)) == NA_INTEGER64){
      |              ~^~~~~~~~~~~~~~~~~~
integer64.c:1006:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
 1006 |     ret[i] = min + ( (long long)(*((unsigned long long *)(&ii))) % d);
      |                                   ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c sort64.c -o sort64.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c sortuse64.c -o sortuse64.o
gcc -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o bit64.so bsearch.o cache.o hash64.o init.o integer64.o sort64.o sortuse64.o -lm -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /tmp/RtmphifQjq/RLIBS_33fecac109801/00LOCK-bit64/00new/bit64/libs
** R
** data
** exec
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (bit64)
* installing *source* package ‘IRanges’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c CompressedList_class.c -o CompressedList_class.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c Grouping_class.c -o Grouping_class.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c IPosRanges_comparison.c -o IPosRanges_comparison.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c IRanges_class.c -o IRanges_class.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c IRanges_constructor.c -o IRanges_constructor.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c NCList.c -o NCList.o
NCList.c:1173:13: warning: ‘NCList_get_y_overlaps_rec’ defined but not used [-Wunused-function]
 1173 | static void NCList_get_y_overlaps_rec(const NCList *x_nclist,
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~
NCList.c:202:22: warning: ‘next_top_down’ defined but not used [-Wunused-function]
  202 | static const NCList *next_top_down(const NCList *nclist)
      |                      ^~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c R_init_IRanges.c -o R_init_IRanges.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c Ranges_class.c -o Ranges_class.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c RleViews_utils.c -o RleViews_utils.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c SimpleIRangesList_class.c -o SimpleIRangesList_class.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c coverage_methods.c -o coverage_methods.o
coverage_methods.c: In function ‘compute_coverage_from_IRanges_holder’:
coverage_methods.c:579:35: warning: ‘x_end’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  579 |         if (*out_ranges_are_tiles && x_end != cvg_len)
      |             ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
coverage_methods.c:495:28: note: ‘x_end’ was declared here
  495 |             i, j, x_start, x_end, shift_elt, tmp;
      |                            ^~~~~
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c extractListFragments.c -o extractListFragments.o
extractListFragments.c: In function ‘C_find_partition_overlaps’:
extractListFragments.c:66:33: warning: ‘split_partitions_buf’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   66 |                                 IntAE_insert_at(split_partitions_buf,
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   67 |                                         IntAE_get_nelt(split_partitions_buf),
      |                                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   68 |                                         q_prev_end);
      |                                         ~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c inter_range_methods.c -o inter_range_methods.o
gcc -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o IRanges.so CompressedAtomicList_utils.o CompressedIRangesList_class.o CompressedList_class.o Grouping_class.o IPosRanges_comparison.o IRanges_class.o IRanges_constructor.o NCList.o R_init_IRanges.o Ranges_class.o RleViews_utils.o S4Vectors_stubs.o SimpleIRangesList_class.o coverage_methods.o extractListFragments.o inter_range_methods.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /tmp/RtmphifQjq/RLIBS_33fecac109801/00LOCK-IRanges/00new/IRanges/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘drop’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘chartr’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘toupper’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘tolower’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘sub’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘gsub’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘startsWith’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘endsWith’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘IRanges’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (IRanges)
* installing *source* package ‘vctrs’ ...
** package ‘vctrs’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c altrep-lazy-character.c -o altrep-lazy-character.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c altrep-rle.c -o altrep-rle.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c altrep.c -o altrep.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c arg-counter.c -o arg-counter.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c arg.c -o arg.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c assert.c -o assert.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c bind.c -o bind.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c c-unchop.c -o c-unchop.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c c.c -o c.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c callables.c -o callables.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c cast-bare.c -o cast-bare.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c cast-dispatch.c -o cast-dispatch.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c cast.c -o cast.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c compare.c -o compare.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c complete.c -o complete.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c conditions.c -o conditions.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c dictionary.c -o dictionary.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c dim.c -o dim.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c empty.c -o empty.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c equal.c -o equal.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c expand.c -o expand.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c fields.c -o fields.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c fill.c -o fill.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c globals.c -o globals.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c group.c -o group.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c growable.c -o growable.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c hash.c -o hash.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c interval.c -o interval.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c match-joint.c -o match-joint.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c match.c -o match.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c missing.c -o missing.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c names.c -o names.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c order-collate.c -o order-collate.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c order-groups.c -o order-groups.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c order-sortedness.c -o order-sortedness.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c order-truelength.c -o order-truelength.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c order.c -o order.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c poly-op.c -o poly-op.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c proxy-restore.c -o proxy-restore.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c proxy.c -o proxy.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c ptype-common.c -o ptype-common.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c ptype.c -o ptype.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c ptype2-dispatch.c -o ptype2-dispatch.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c ptype2.c -o ptype2.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c rank.c -o rank.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c rep.c -o rep.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c rlang-dev.c -o rlang-dev.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c rlang.c -o rlang.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c runs.c -o runs.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c set.c -o set.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c shape.c -o shape.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c size-common.c -o size-common.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c size.c -o size.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c slice-array.c -o slice-array.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c slice-assign-array.c -o slice-assign-array.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c slice-assign.c -o slice-assign.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c slice-chop.c -o slice-chop.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c slice-interleave.c -o slice-interleave.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c slice.c -o slice.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c split.c -o split.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c subscript-loc.c -o subscript-loc.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c subscript.c -o subscript.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c translate.c -o translate.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c type-data-frame.c -o type-data-frame.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c type-date-time.c -o type-date-time.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c type-factor.c -o type-factor.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c type-info.c -o type-info.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c type-integer64.c -o type-integer64.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c type-tibble.c -o type-tibble.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c typeof2-s3.c -o typeof2-s3.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c typeof2.c -o typeof2.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c unspecified.c -o unspecified.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c utils-dispatch.c -o utils-dispatch.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c utils.c -o utils.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c vctrs-core.c -o vctrs-core.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c version.c -o version.o
gcc -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o vctrs.so altrep-lazy-character.o altrep-rle.o altrep.o arg-counter.o arg.o assert.o bind.o c-unchop.o c.o callables.o cast-bare.o cast-dispatch.o cast.o compare.o complete.o conditions.o dictionary.o dim.o empty.o equal.o expand.o fields.o fill.o globals.o group.o growable.o hash.o init.o interval.o match-joint.o match.o missing.o names.o order-collate.o order-groups.o order-sortedness.o order-truelength.o order.o poly-op.o proxy-restore.o proxy.o ptype-common.o ptype.o ptype2-dispatch.o ptype2.o rank.o rep.o rlang-dev.o rlang.o runs.o set.o shape.o size-common.o size.o slice-array.o slice-assign-array.o slice-assign.o slice-chop.o slice-interleave.o slice.o split.o subscript-loc.o subscript.o translate.o type-data-frame.o type-date-time.o type-factor.o type-info.o type-integer64.o type-tibble.o typeof2-s3.o typeof2.o unspecified.o utils-dispatch.o utils.o vctrs-core.o version.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /tmp/RtmphifQjq/RLIBS_33fecac109801/00LOCK-vctrs/00new/vctrs/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (vctrs)
* installing *source* package ‘openssl’ ...
** package ‘openssl’ successfully unpacked and MD5 sums checked
** using staged installation
Found pkg-config cflags and libs!
Using PKG_CFLAGS=
Using PKG_LIBS=-l:libssl.so.3 -l:libcrypto.so.3
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
rm -f aes.o base64.o bignum.o cert.o compatibility.o diffie.o envelope.o error.o hash.o info.o keygen.o keys.o onload.o openssh.o password.o pbkdf.o pem.o pkcs12.o pkcs7.o rand.o rsa.o signing.o ssl.o stream.o write.o x25519.o openssl.so bcrypt/libstatbcrypt.a bcrypt/bcrypt_pbkdf.o bcrypt/blowfish.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c aes.c -o aes.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c base64.c -o base64.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c bignum.c -o bignum.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c cert.c -o cert.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c compatibility.c -o compatibility.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c diffie.c -o diffie.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c envelope.c -o envelope.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c error.c -o error.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c hash.c -o hash.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c info.c -o info.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c keygen.c -o keygen.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c keys.c -o keys.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c onload.c -o onload.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c openssh.c -o openssh.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c password.c -o password.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c pbkdf.c -o pbkdf.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c pem.c -o pem.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c pkcs12.c -o pkcs12.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c pkcs7.c -o pkcs7.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c rand.c -o rand.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c rsa.c -o rsa.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c signing.c -o signing.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c ssl.c -o ssl.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c stream.c -o stream.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c write.c -o write.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c x25519.c -o x25519.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c bcrypt/bcrypt_pbkdf.c -o bcrypt/bcrypt_pbkdf.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c bcrypt/blowfish.c -o bcrypt/blowfish.o
ar rcs bcrypt/libstatbcrypt.a bcrypt/bcrypt_pbkdf.o bcrypt/blowfish.o
gcc -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o openssl.so aes.o base64.o bignum.o cert.o compatibility.o diffie.o envelope.o error.o hash.o info.o keygen.o keys.o onload.o openssh.o password.o pbkdf.o pem.o pkcs12.o pkcs7.o rand.o rsa.o signing.o ssl.o stream.o write.o x25519.o -Lbcrypt -lstatbcrypt -l:libssl.so.3 -l:libcrypto.so.3 -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /tmp/RtmphifQjq/RLIBS_33fecac109801/00LOCK-openssl/00new/openssl/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (openssl)
* installing *source* package ‘XVector’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c RDS_random_access.c -o RDS_random_access.o
RDS_random_access.c: In function ‘RDS_extract_subarray’:
RDS_random_access.c:796:25: warning: unused variable ‘ans’ [-Wunused-variable]
  796 |         SEXP subscript, ans;
      |                         ^~~
RDS_random_access.c:793:18: warning: variable ‘x_type’ set but not used [-Wunused-but-set-variable]
  793 |         SEXPTYPE x_type;
      |                  ^~~~~~
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c R_init_XVector.c -o R_init_XVector.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c SharedDouble_class.c -o SharedDouble_class.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c SharedInteger_class.c -o SharedInteger_class.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c SharedRaw_class.c -o SharedRaw_class.o
SharedRaw_class.c: In function ‘SharedRaw_read_complexes_from_subscript’:
SharedRaw_class.c:396:20: warning: variable ‘src_tag’ set but not used [-Wunused-but-set-variable]
  396 |         SEXP dest, src_tag;
      |                    ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c SharedVector_class.c -o SharedVector_class.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c XDouble_class.c -o XDouble_class.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c XInteger_class.c -o XInteger_class.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c XRawList_comparison.c -o XRawList_comparison.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c XRaw_class.c -o XRaw_class.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c XVectorList_class.c -o XVectorList_class.o
XVectorList_class.c: In function ‘_new_XRawList_from_CharAEAE’:
XVectorList_class.c:459:17: warning: ‘lkup_length’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  459 |                 _Ocopy_bytes_to_i1i2_with_lkup(0, dest.length - 1,
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  460 |                         (char *) dest.ptr, dest.length,
      |                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  461 |                         src->elts, CharAE_get_nelt(src),
      |                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  462 |                         lkup0, lkup_length);
      |                         ~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c XVector_class.c -o XVector_class.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c io_utils.c -o io_utils.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c slice_methods.c -o slice_methods.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c vector_copy.c -o vector_copy.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c view_summarization_methods.c -o view_summarization_methods.o
view_summarization_methods.c: In function ‘get_which_min_from_Ints_holder’:
view_summarization_methods.c:219:45: warning: ‘cur_min’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  219 |                 if (which_min == NA_INTEGER || x < cur_min) {
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
view_summarization_methods.c: In function ‘get_which_min_from_Doubles_holder’:
view_summarization_methods.c:246:45: warning: ‘cur_min’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  246 |                 if (which_min == NA_INTEGER || x < cur_min) {
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
view_summarization_methods.c: In function ‘get_which_max_from_Ints_holder’:
view_summarization_methods.c:269:45: warning: ‘cur_max’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  269 |                 if (which_max == NA_INTEGER || x > cur_max) {
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
view_summarization_methods.c: In function ‘get_which_max_from_Doubles_holder’:
view_summarization_methods.c:296:45: warning: ‘cur_max’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  296 |                 if (which_max == NA_INTEGER || x > cur_max) {
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o XVector.so IRanges_stubs.o Ocopy_byteblocks.o RDS_random_access.o R_init_XVector.o S4Vectors_stubs.o SharedDouble_class.o SharedInteger_class.o SharedRaw_class.o SharedVector_class.o XDouble_class.o XInteger_class.o XRawList_comparison.o XRaw_class.o XVectorList_class.o XVector_class.o io_utils.o slice_methods.o vector_copy.o view_summarization_methods.o -lz -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /tmp/RtmphifQjq/RLIBS_33fecac109801/00LOCK-XVector/00new/XVector/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (XVector)
* installing *source* package ‘GenomeInfoDb’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GenomeInfoDb)
* installing *source* package ‘memoise’ ...
** package ‘memoise’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (memoise)
* installing *source* package ‘blob’ ...
** package ‘blob’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (blob)
* installing *source* package ‘httr’ ...
** package ‘httr’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (httr)
* installing *source* package ‘Biostrings’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c BAB_class.c -o BAB_class.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c BitMatrix.c -o BitMatrix.o
BitMatrix.c:299:13: warning: ‘BitMatrix_print’ defined but not used [-Wunused-function]
  299 | static void BitMatrix_print(BitMatrix *bitmat)
      |             ^~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c MIndex_class.c -o MIndex_class.o
MIndex_class.c: In function ‘SparseMIndex_endIndex’:
MIndex_class.c:184:27: warning: unused variable ‘poffsets_order’ [-Wunused-variable]
  184 |         IntAE *poffsets, *poffsets_order;
      |                           ^~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c SparseList_utils.c -o SparseList_utils.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c XStringSetList_class.c -o XStringSetList_class.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c XStringSet_class.c -o XStringSet_class.o
XStringSet_class.c: In function ‘new_XStringSet_from_CHARACTER’:
XStringSet_class.c:124:17: warning: ‘lkup_len’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  124 |                 _copy_CHARSXP_to_Chars_holder(&ans_elt_holder, x_elt,
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  125 |                                 INTEGER(start)[i], lkup0, lkup_len);
      |                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c XString_class.c -o XString_class.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c align_needwunsQS.c -o align_needwunsQS.o
align_needwunsQS.c: In function ‘align_needwunsQS’:
align_needwunsQS.c:155:29: warning: ‘sc’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  155 |         INTEGER(ans_elt)[0] = score;
      |         ~~~~~~~~~~~~~~~~~~~~^~~~~~~
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c align_utils.c -o align_utils.o
align_utils.c: In function ‘PairwiseAlignmentsSingleSubject_align_aligned’:
align_utils.c:250:42: warning: ‘indelWidthSubject’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  250 |                                 jPattern += indelWidthSubject;
      |                                 ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
align_utils.c:231:63: warning: ‘indelStartSubject’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  231 |                         if ((numberOfIndelSubject == 0) || (j < indelStartSubject)) {
      |                                                            ~~~^~~~~~~~~~~~~~~~~~~~
align_utils.c:239:72: warning: ‘indelWidthPattern’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  239 |                                                 mappedStringPtr[index] = gapCodeValue;
      |                                                 ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
align_utils.c:232:78: warning: ‘indelStartPattern’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  232 |                                 if ((numberOfIndelPattern == 0) || (jPattern < indelStartPattern)) {
      |                                                                    ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c find_palindromes.c -o find_palindromes.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c gtestsim.c -o gtestsim.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c inject_code.c -o inject_code.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c letter_frequency.c -o letter_frequency.o
letter_frequency.c: In function ‘XStringSet_two_way_letter_frequency’:
letter_frequency.c:957:48: warning: unused variable ‘x_pos’ [-Wunused-variable]
  957 |   int x_width, y_width, x_length, *ans_mat, i, x_pos;
      |                                                ^~~~~
letter_frequency.c:956:13: warning: unused variable ‘ans_dimnames’ [-Wunused-variable]
  956 |   SEXP ans, ans_dimnames;
      |             ^~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c lowlevel_matching.c -o lowlevel_matching.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c match_PWM.c -o match_PWM.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c match_pattern.c -o match_pattern.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c match_pattern_indels.c -o match_pattern_indels.o
match_pattern_indels.c:7:13: warning: ‘test_match_pattern_indels’ defined but not used [-Wunused-function]
    7 | static void test_match_pattern_indels(const char *p, const char *s,
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c match_pdict.c -o match_pdict.o
match_pdict.c: In function ‘vmatch_PDict3Parts_XStringSet’:
match_pdict.c:419:33: warning: ‘ans_col’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  419 |                         ans_col += tb_length;
      |                         ~~~~~~~~^~~~~~~~~~~~
match_pdict.c:392:65: note: ‘ans_col’ was declared here
  392 |         int tb_length, S_length, collapse0, i, j, match_count, *ans_col;
      |                                                                 ^~~~~~~
match_pdict.c: In function ‘vmatch_XStringSet_XStringSet’:
match_pdict.c:470:41: warning: ‘ans_elt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  470 |                                 ans_elt += P_length;
      |                                 ~~~~~~~~^~~~~~~~~~~
match_pdict.c:441:64: note: ‘ans_elt’ was declared here
  441 |         int P_length, S_length, collapse0, i, j, match_count, *ans_elt;
      |                                                                ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
match_pdict_ACtree2.c: In function ‘split_and_move_pointers’:
match_pdict_ACtree2.c:1031:17: warning: variable ‘node0’ set but not used [-Wunused-but-set-variable]
 1031 |         ACnode *node0, *node1, *node2;
      |                 ^~~~~
match_pdict_ACtree2.c: In function ‘merge_pointers’:
match_pdict_ACtree2.c:1076:17: warning: variable ‘node0’ set but not used [-Wunused-but-set-variable]
 1076 |         ACnode *node0, *node1, *node2;
      |                 ^~~~~
At top level:
match_pdict_ACtree2.c:602:21: warning: ‘a_nice_max_nodeextbuf_nelt’ defined but not used [-Wunused-function]
  602 | static unsigned int a_nice_max_nodeextbuf_nelt(int nnodes)
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~
match_pdict_ACtree2.c:139:13: warning: ‘debug_node_counting_functions’ defined but not used [-Wunused-function]
  139 | static void debug_node_counting_functions(int maxdepth)
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c match_pdict_Twobit.c -o match_pdict_Twobit.o
match_pdict_Twobit.c: In function ‘build_Twobit’:
match_pdict_Twobit.c:75:27: warning: ‘twobit_sign2pos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   75 |         PROTECT(ans_elt = new_XInteger_from_tag("XInteger", twobit_sign2pos));
      |                           ^~~~~~~~~~~~~~~~~~~~~
match_pdict_Twobit.c:110:19: note: ‘twobit_sign2pos’ was declared here
  110 |         SEXP ans, twobit_sign2pos;
      |                   ^~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c match_pdict_utils.c -o match_pdict_utils.o
match_pdict_utils.c: In function ‘match_ppheadtail0’:
match_pdict_utils.c:653:56: warning: unused variable ‘ncol’ [-Wunused-variable]
  653 |         int nelt, min_safe_tb_end, max_safe_tb_end, j, ncol;
      |                                                        ^~~~
match_pdict_utils.c: In function ‘match_ppheadtail’:
match_pdict_utils.c:713:13: warning: unused variable ‘nelt’ [-Wunused-variable]
  713 |         int nelt, nkey0, nkey1, nkey2, i, key;
      |             ^~~~
match_pdict_utils.c: In function ‘_match_pdict_all_flanks’:
match_pdict_utils.c:820:51: warning: unused variable ‘subtotal_NFC’ [-Wunused-variable]
  820 |         static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
      |                                                   ^~~~~~~~~~~~
match_pdict_utils.c:820:34: warning: unused variable ‘total_NFC’ [-Wunused-variable]
  820 |         static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
      |                                  ^~~~~~~~~
match_pdict_utils.c:819:40: warning: unused variable ‘NFC’ [-Wunused-variable]
  819 |         unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
      |                                        ^~~
match_pdict_utils.c:819:33: warning: unused variable ‘nloci’ [-Wunused-variable]
  819 |         unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
      |                                 ^~~~~
match_pdict_utils.c:819:27: warning: unused variable ‘ndup’ [-Wunused-variable]
  819 |         unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
      |                           ^~~~
At top level:
match_pdict_utils.c:820:34: warning: ‘total_NFC’ defined but not used [-Wunused-variable]
  820 |         static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
      |                                  ^~~~~~~~~
match_pdict_utils.c:820:51: warning: ‘subtotal_NFC’ defined but not used [-Wunused-variable]
  820 |         static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
      |                                                   ^~~~~~~~~~~~
match_pdict_utils.c:261:13: warning: ‘match_headtail_by_loc’ defined but not used [-Wunused-function]
  261 | static void match_headtail_by_loc(const HeadTail *headtail,
      |             ^~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c match_reporting.c -o match_reporting.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c matchprobes.c -o matchprobes.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c pmatchPattern.c -o pmatchPattern.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c read_fasta_files.c -o read_fasta_files.o
In function ‘new_FASTAloaderExt’,
    inlined from ‘read_fasta_files’ at read_fasta_files.c:432:15:
read_fasta_files.c:188:16: warning: ‘loader_ext.seq_elt_holder.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
  188 |         return loader_ext;
      |                ^~~~~~~~~~
read_fasta_files.c: In function ‘read_fasta_files’:
read_fasta_files.c:184:24: note: ‘loader_ext’ declared here
  184 |         FASTAloaderExt loader_ext;
      |                        ^~~~~~~~~~
In function ‘new_FASTAloaderExt’,
    inlined from ‘read_fasta_files’ at read_fasta_files.c:432:15:
read_fasta_files.c:188:16: warning: ‘loader_ext.seq_elt_holder.length’ may be used uninitialized [-Wmaybe-uninitialized]
  188 |         return loader_ext;
      |                ^~~~~~~~~~
read_fasta_files.c: In function ‘read_fasta_files’:
read_fasta_files.c:184:24: note: ‘loader_ext’ declared here
  184 |         FASTAloaderExt loader_ext;
      |                        ^~~~~~~~~~
In function ‘new_FASTAloaderExt’,
    inlined from ‘read_fasta_blocks’ at read_fasta_files.c:598:15:
read_fasta_files.c:188:16: warning: ‘loader_ext.seq_elt_holder.ptr’ is used uninitialized [-Wuninitialized]
  188 |         return loader_ext;
      |                ^~~~~~~~~~
read_fasta_files.c: In function ‘read_fasta_blocks’:
read_fasta_files.c:184:24: note: ‘loader_ext’ declared here
  184 |         FASTAloaderExt loader_ext;
      |                        ^~~~~~~~~~
In function ‘new_FASTAloaderExt’,
    inlined from ‘read_fasta_blocks’ at read_fasta_files.c:598:15:
read_fasta_files.c:188:16: warning: ‘loader_ext.seq_elt_holder.length’ is used uninitialized [-Wuninitialized]
  188 |         return loader_ext;
      |                ^~~~~~~~~~
read_fasta_files.c: In function ‘read_fasta_blocks’:
read_fasta_files.c:184:24: note: ‘loader_ext’ declared here
  184 |         FASTAloaderExt loader_ext;
      |                        ^~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c read_fastq_files.c -o read_fastq_files.o
read_fastq_files.c: In function ‘parse_FASTQ_file’:
read_fastq_files.c:394:28: warning: ‘dont_load’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  394 |                         if (dont_load || loader->new_empty_seq_hook == NULL)
      |                            ^
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c replaceAt.c -o replaceAt.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c replace_letter_at.c -o replace_letter_at.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c strutils.c -o strutils.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c translate.c -o translate.o
translate.c: In function ‘DNAStringSet_translate’:
translate.c:110:36: warning: ‘if_ambig0’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  110 |                                 if (if_ambig == TRANSLATE_ERROR) {
      |                                    ^
translate.c:136:36: note: ‘if_ambig0’ was declared here
  136 |         int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode;
      |                                    ^~~~~~~~~
translate.c:106:36: warning: ‘if_non_ambig0’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  106 |                                 if (if_non_ambig == TRANSLATE_TO_X)
      |                                    ^
translate.c:136:21: note: ‘if_non_ambig0’ was declared here
  136 |         int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode;
      |                     ^~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c unstrsplit_methods.c -o unstrsplit_methods.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c utils.c -o utils.o
utils.c: In function ‘_get_twobit_signature’:
utils.c:157:16: warning: ‘twobit_sign’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  157 |         return twobit_sign;
      |                ^~~~~~~~~~~
utils.c: In function ‘_get_twobit_signature_at’:
utils.c:164:19: warning: ‘twobit_sign’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  164 |         int i, j, twobit_sign;
      |                   ^~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include' -I'/tmp/RtmphifQjq/RLIBS_33fecac109801/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c xscat.c -o xscat.o
In file included from /tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include/S4Vectors_defines.h:18,
                 from /tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include/IRanges_defines.h:18,
                 from ../inst/include/Biostrings_defines.h:18,
                 from Biostrings.h:1,
                 from xscat.c:1:
xscat.c: In function ‘XString_xscat’:
/home/biocbuild/bbs-3.18-bioc/R/include/Rdefines.h:91:33: warning: ‘ans_length’ may be used uninitialized [-Wmaybe-uninitialized]
   91 | #define NEW_RAW(n)              Rf_allocVector(RAWSXP,n)
      |                                 ^~~~~~~~~~~~~~
xscat.c:18:20: note: ‘ans_length’ was declared here
   18 |         int nargs, ans_length, tag_offset, j;
      |                    ^~~~~~~~~~
xscat.c:52:23: warning: ‘ans_classname’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   52 |         PROTECT(ans = new_XRaw_from_tag(ans_classname, ans_tag));
      |                       ^~~~~~~~~~~~~~~~~
In file included from /tmp/RtmphifQjq/RLIBS_33fecac109801/S4Vectors/include/S4Vectors_defines.h:18,
                 from /tmp/RtmphifQjq/RLIBS_33fecac109801/IRanges/include/IRanges_defines.h:18,
                 from ../inst/include/Biostrings_defines.h:18,
                 from Biostrings.h:1,
                 from xscat.c:1:
xscat.c: In function ‘XStringSet_xscat’:
/home/biocbuild/bbs-3.18-bioc/R/include/Rdefines.h:85:33: warning: ‘ans_length’ may be used uninitialized [-Wmaybe-uninitialized]
   85 | #define NEW_INTEGER(n)          Rf_allocVector(INTSXP,n)
      |                                 ^~~~~~~~~~~~~~
xscat.c:66:39: note: ‘ans_length’ was declared here
   66 |         int nargs, *arg_lengths, *ii, ans_length, i, j, *width;
      |                                       ^~~~~~~~~~
xscat.c:108:23: warning: ‘ans_element_type’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  108 |         PROTECT(ans = _alloc_XStringSet(ans_element_type, ans_width));
      |                       ^~~~~~~~~~~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o Biostrings.so BAB_class.o BitMatrix.o IRanges_stubs.o MIndex_class.o PreprocessedTB_class.o R_init_Biostrings.o RoSeqs_utils.o S4Vectors_stubs.o SparseList_utils.o XStringSetList_class.o XStringSet_class.o XString_class.o XVector_stubs.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o find_palindromes.o gtestsim.o inject_code.o letter_frequency.o lowlevel_matching.o match_PWM.o match_pattern.o match_pattern_boyermoore.o match_pattern_indels.o match_pattern_shiftor.o match_pdict.o match_pdict_ACtree2.o match_pdict_Twobit.o match_pdict_utils.o match_reporting.o matchprobes.o pmatchPattern.o read_fasta_files.o read_fastq_files.o replaceAt.o replace_letter_at.o strutils.o translate.o unstrsplit_methods.o utils.o xscat.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /tmp/RtmphifQjq/RLIBS_33fecac109801/00LOCK-Biostrings/00new/Biostrings/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for ‘twoWayAlphabetFrequencyByQuality’ with signature ‘"QualityScaledXStringSet"’: no definition for class “QualityScaledXStringSet”
Creating a new generic function for ‘strsplit’ in package ‘Biostrings’
Creating a generic function for ‘ls’ from package ‘base’ in package ‘Biostrings’
Creating a new generic function for ‘pattern’ in package ‘Biostrings’
Creating a new generic function for ‘offset’ in package ‘Biostrings’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Biostrings)
ERROR: dependencies ‘plogr’, ‘cpp11’ are not available for package ‘RSQLite’
* removing ‘/tmp/RtmphifQjq/RLIBS_33fecac109801/RSQLite’
Warning in install.packages(cdfname, lib = lib, repos = repositories(),  :
  installation of package ‘RSQLite’ had non-zero exit status
* installing *source* package ‘KEGGREST’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (KEGGREST)
ERROR: dependency ‘RSQLite’ is not available for package ‘AnnotationDbi’
* removing ‘/tmp/RtmphifQjq/RLIBS_33fecac109801/AnnotationDbi’
Warning in install.packages(cdfname, lib = lib, repos = repositories(),  :
  installation of package ‘AnnotationDbi’ had non-zero exit status
ERROR: dependency ‘AnnotationDbi’ is not available for package ‘hgu95acdf’
* removing ‘/tmp/RtmphifQjq/RLIBS_33fecac109801/hgu95acdf’
Warning in install.packages(cdfname, lib = lib, repos = repositories(),  :
  installation of package ‘hgu95acdf’ had non-zero exit status

The downloaded source packages are in
	‘/tmp/RtmpD0IhET/downloaded_packages’
Error in getCdfInfo(object) : 
  Could not obtain CDF environment, problems encountered:
Specified environment does not contain hgu95a
Library - package hgu95acdf not installed
Library - package hgu95acdf not installed
Calls: logitTAffy -> featureNames -> featureNames -> getCdfInfo
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘logitT.Rnw’... failed
 ERROR
Errors in running code in vignettes:
when running code in ‘logitT.Rnw’
  ...

The downloaded source packages are in
	‘/tmp/RtmpaUONL8/downloaded_packages’

  When sourcing ‘logitT.R’:
Error: Could not obtain CDF environment, problems encountered:
Specified environment does not contain hgu95a
Library - package hgu95acdf not installed
Library - package hgu95acdf not installed
Execution halted

* checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
--- re-building ‘logitT.Rnw’ using Sweave
Loading required package: affy
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Warning: Package 'logitT' is deprecated and will be removed from Bioconductor
  version 3.19
also installing the dependencies ‘RSQLite’, ‘AnnotationDbi’

trying URL 'https://cloud.r-project.org/src/contrib/RSQLite_2.3.5.tar.gz'
Content type 'application/x-gzip' length 4247252 bytes (4.1 MB)
==================================================
downloaded 4.1 MB

trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/AnnotationDbi_1.64.1.tar.gz'
Content type 'application/x-gzip' length 4359564 bytes (4.2 MB)
==================================================
downloaded 4.2 MB

trying URL 'https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgu95acdf_2.18.0.tar.gz'
Content type 'application/x-gzip' length 1331364 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

ERROR: dependencies ‘plogr’, ‘cpp11’ are not available for package ‘RSQLite’
* removing ‘/tmp/RtmphifQjq/RLIBS_33fecac109801/RSQLite’
Warning in install.packages(cdfname, lib = lib, repos = repositories(),  :
  installation of package ‘RSQLite’ had non-zero exit status
ERROR: dependency ‘RSQLite’ is not available for package ‘AnnotationDbi’
* removing ‘/tmp/RtmphifQjq/RLIBS_33fecac109801/AnnotationDbi’
Warning in install.packages(cdfname, lib = lib, repos = repositories(),  :
  installation of package ‘AnnotationDbi’ had non-zero exit status
ERROR: dependency ‘AnnotationDbi’ is not available for package ‘hgu95acdf’
* removing ‘/tmp/RtmphifQjq/RLIBS_33fecac109801/hgu95acdf’
Warning in install.packages(cdfname, lib = lib, repos = repositories(),  :
  installation of package ‘hgu95acdf’ had non-zero exit status

The downloaded source packages are in
	‘/tmp/RtmpHxIe9v/downloaded_packages’

Error: processing vignette 'logitT.Rnw' failed with diagnostics:
 chunk 2 
Error in getCdfInfo(object) : 
  Could not obtain CDF environment, problems encountered:
Specified environment does not contain hgu95a
Library - package hgu95acdf not installed
Library - package hgu95acdf not installed

--- failed re-building ‘logitT.Rnw’

SUMMARY: processing the following file failed:
  ‘logitT.Rnw’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/logitT.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL logitT
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘logitT’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c logitTfunc.c -o logitTfunc.o
gcc -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o logitT.so logitTfunc.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.18-bioc/R/site-library/00LOCK-logitT/00new/logitT/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'logitT' is deprecated and will be removed from Bioconductor
  version 3.19
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: Package 'logitT' is deprecated and will be removed from Bioconductor
  version 3.19
** testing if installed package keeps a record of temporary installation path
* DONE (logitT)