Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-06-11 14:39 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4522
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4468
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 702/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
farms 1.56.0  (landing page)
Djork-Arne Clevert
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/farms
git_branch: RELEASE_3_19
git_last_commit: d304548
git_last_commit_date: 2024-04-30 10:22:32 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for farms on nebbiolo1

To the developers/maintainers of the farms package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/farms.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: farms
Version: 1.56.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:farms.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings farms_1.56.0.tar.gz
StartedAt: 2024-06-09 22:57:57 -0400 (Sun, 09 Jun 2024)
EndedAt: 2024-06-09 23:03:34 -0400 (Sun, 09 Jun 2024)
EllapsedTime: 336.7 seconds
RetCode: 1
Status:   ERROR  
CheckDir: farms.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:farms.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings farms_1.56.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/farms.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* 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 ‘farms/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘farms’ version ‘1.56.0’
* checking package namespace information ... NOTE
  Namespace with empty importFrom: ‘methods’
* 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 ‘farms’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘affy’ ‘MASS’ ‘methods’ ‘Biobase’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  ‘affy’ ‘methods’
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘Biobase’ ‘utils’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespaces in Imports field not imported from:
  ‘Biobase’ ‘MASS’
  All declared Imports should be used.
Package in Depends field not imported from: ‘MASS’
  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
File ‘farms/R/zzz.R’:
  .onLoad calls:
    require("methods", quietly = TRUE)
    packageStartupMessage(" _                             ", "\n",     "| |                            ", "\n", "| |  __,   ,_    _  _  _    ,  ",     "\n", "|/  /  |  /  |  / |/ |/ |  / \\_", "\n", "|__/\\_/|_/   |_/  |  |  |_/ \\/ ",     "\n", "|\\                             ", "\n", "|/   ",     "\n")
    require(utils)
    require(Biobase, quietly = TRUE)
    require(affy, quietly = TRUE)
    packageStartupMessage("Citation: S. Hochreiter et al.,", "\n",     "A new summarization method for affymetrix probe level data,",     "\n", "Bioinformatics, 22, 8, 943-949, 2006", "\n", "\n",     "Citation: W. Talloen et al.,", "\n", "I/NI-calls for the exclusion of non-informative genes: a highly effective filtering tool for microarray data,",     "\n", "Bioinformatics, 23, 21, 2897-2902, 2007", "\n", "BibTex: enter 'toBibtex(citation(\"farms\"))'",     "\n\n", "Homepage: http://www.bioinf.jku.at/software/farms/farms.html",     "\n\n", "FARMS Package Version ", version, "\n")
    packageStartupMessage("\n", "Changes in FARMS:", "\n", "For all changes previous to 1.3.0, see the farms vignette.",     "\n", "Version 1.3.0: Added I/NI-calls for filtering", "\n",     "               Adjusted Hyperparameters for alternative CDFs,",     "\n", "               probes set standardized, weighted mean",     "\n", "               Works now with R >= 2.8 and Bioconductor 2.3,",     "\n", "               Changed termination criterion, initialization values,",     "\n", "               factors and loadings scaled, added argument robust",     "\n", "               Update for R-2.11", "\n", "               Updated I/NI-Call for Laplace-FARMS version,",     "\n", "               Maximum likelihood correlation structure given",     "\n", "               non-negative constraints", "\n", "Version 1.4.0: Default centering changed to median",     "\n", "Version 1.8.x: Suppression of spurious correlation (Laplace-FARMS)",     "\n")

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

plot,INI_Calls-missing: no visible global function definition for
  ‘truehist’
Undefined global functions or variables:
  truehist
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘farms.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, 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")'.

Loading required package: MASS
 _                             
| |                            
| |  __,   ,_    _  _  _    ,  
|/  /  |  /  |  / |/ |/ |  / \_
|__/\_/|_/   |_/  |  |  |_/ \/ 
|\                             
|/   

Citation: S. Hochreiter et al.,
A new summarization method for affymetrix probe level data,
Bioinformatics, 22, 8, 943-949, 2006

Citation: W. Talloen et al.,
I/NI-calls for the exclusion of non-informative genes: a highly effective filtering tool for microarray data,
Bioinformatics, 23, 21, 2897-2902, 2007
BibTex: enter 'toBibtex(citation("farms"))'

Homepage: http://www.bioinf.jku.at/software/farms/farms.html

FARMS Package Version 1.56.0


Changes in FARMS:
For all changes previous to 1.3.0, see the farms vignette.
Version 1.3.0: Added I/NI-calls for filtering
               Adjusted Hyperparameters for alternative CDFs,
               probes set standardized, weighted mean
               Works now with R >= 2.8 and Bioconductor 2.3,
               Changed termination criterion, initialization values,
               factors and loadings scaled, added argument robust
               Update for R-2.11
               Updated I/NI-Call for Laplace-FARMS version,
               Maximum likelihood correlation structure given
               non-negative constraints
Version 1.4.0: Default centering changed to median
Version 1.8.x: Suppression of spurious correlation (Laplace-FARMS)

Warning in fun(libname, pkgname) :
  Package 'farms' is deprecated and will be removed from
  Bioconductor version 3.20
also installing the dependencies ‘sys’, ‘cli’, ‘glue’, ‘lifecycle’, ‘fastmap’, ‘askpass’, ‘UCSC.utils’, ‘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-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c exec.c -o exec.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o sys.so exec.o init.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/00LOCK-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 ‘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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-bioc/R/lib -lR
installing to /tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/00LOCK-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-3.19-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-3.19-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-3.19-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-3.19-bioc/R/lib -L/usr/local/lib -o glue.so glue.o init.o trim.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/00LOCK-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-3.19-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-3.19-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-3.19-bioc/R/lib -L/usr/local/lib -o fastmap.so fastmap.o init.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/00LOCK-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-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c attrutil.c -o attrutil.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c bit.c -o bit.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c chunkutil.c -o chunkutil.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c clone.c -o clone.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c integerutil.c -o integerutil.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c merge.c -o merge.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c rle.c -o rle.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c sort.c -o sort.o
gcc -shared -L/home/biocbuild/bbs-3.19-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-3.19-bioc/R/lib -lR
installing to /tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/00LOCK-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-bioc/R/lib -lR
installing to /tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/00LOCK-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-bioc/R/lib -lR
installing to /tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/00LOCK-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-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c rawmatch.c -o rawmatch.o
gcc -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o mime.so init.o rawmatch.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/00LOCK-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-bioc/R/lib -L/usr/local/lib -o rlang.so capture.o internal.o rlang.o version.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/00LOCK-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-3.19-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-3.19-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-3.19-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-3.19-bioc/R/lib -L/usr/local/lib -o png.so dummy.o read.o write.o -lpng16 -lm -lz -lm -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/00LOCK-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-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c AEbufs.c -o AEbufs.o
gcc -I"/home/biocbuild/bbs-3.19-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-3.19-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-3.19-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-3.19-bioc/R/include/Rinternals.h:893:33: warning: ‘revmap’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  893 | #define defineVar               Rf_defineVar
      |                                 ^~~~~~~~~~~~
Hits_class.c:216:19: note: ‘revmap’ was declared here
  216 |         SEXP ans, revmap, symbol;
      |                   ^~~~~~
gcc -I"/home/biocbuild/bbs-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c anyMissing.c -o anyMissing.o
gcc -I"/home/biocbuild/bbs-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-bioc/R/lib -lR
installing to /tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/00LOCK-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-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c askpass.c -o askpass.o
gcc -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o askpass.so askpass.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/00LOCK-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 ‘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-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c cache.c -o cache.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o cachem.so cache.o init.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/00LOCK-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-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c bsearch.c -o bsearch.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c cache.c -o cache.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c hash64.c -o hash64.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c sort64.c -o sort64.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c sortuse64.c -o sortuse64.o
gcc -shared -L/home/biocbuild/bbs-3.19-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-3.19-bioc/R/lib -lR
installing to /tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/00LOCK-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-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c CompressedList_class.c -o CompressedList_class.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c Grouping_class.c -o Grouping_class.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c IPosRanges_comparison.c -o IPosRanges_comparison.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c IRanges_class.c -o IRanges_class.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c IRanges_constructor.c -o IRanges_constructor.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/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-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/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-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c Ranges_class.c -o Ranges_class.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c RleViews_utils.c -o RleViews_utils.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c SimpleIRangesList_class.c -o SimpleIRangesList_class.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/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-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/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-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/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-3.19-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-3.19-bioc/R/lib -lR
installing to /tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/00LOCK-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-bioc/R/lib -lR
installing to /tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/00LOCK-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-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-3.19-bioc/R/lib -lR
installing to /tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/00LOCK-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-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/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-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/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-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c SharedDouble_class.c -o SharedDouble_class.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c SharedInteger_class.c -o SharedInteger_class.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/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-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c SharedVector_class.c -o SharedVector_class.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c XDouble_class.c -o XDouble_class.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c XInteger_class.c -o XInteger_class.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c XRawList_comparison.c -o XRawList_comparison.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c XRaw_class.c -o XRaw_class.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/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-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c XVector_class.c -o XVector_class.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c io_utils.c -o io_utils.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c slice_methods.c -o slice_methods.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c vector_copy.c -o vector_copy.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/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-3.19-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-3.19-bioc/R/lib -lR
installing to /tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/00LOCK-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 ‘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 ‘UCSC.utils’ ...
** 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 (UCSC.utils)
ERROR: dependencies ‘plogr’, ‘cpp11’ are not available for package ‘RSQLite’
* removing ‘/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/RSQLite’
Warning in install.packages(cdfname, lib = lib, repos = repositories(),  :
  installation of package ‘RSQLite’ had non-zero exit status
* 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 ‘Biostrings’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c BAB_class.c -o BAB_class.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/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-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/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-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/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-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c SparseList_utils.c -o SparseList_utils.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c XStringSetList_class.c -o XStringSetList_class.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/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-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c XString_class.c -o XString_class.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c find_palindromes.c -o find_palindromes.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c gtestsim.c -o gtestsim.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c inject_code.c -o inject_code.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/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;
      |                                                ^~~~~
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c lowlevel_matching.c -o lowlevel_matching.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c match_PWM.c -o match_PWM.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c match_pattern.c -o match_pattern.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/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-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/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-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/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-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/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-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/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-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/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-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/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-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c match_reporting.c -o match_reporting.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c matchprobes.c -o matchprobes.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c pmatchPattern.c -o pmatchPattern.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c read_fasta_files.c -o read_fasta_files.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/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-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c replaceAt.c -o replaceAt.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/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-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c strutils.c -o strutils.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/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-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c unstrsplit_methods.c -o unstrsplit_methods.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/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-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/IRanges/include' -I'/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c xscat.c -o xscat.o
In file included from /tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include/S4Vectors_defines.h:18,
                 from /tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/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-3.19-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/RtmpLl4NmO/RLIBS_272a344e7359f1/S4Vectors/include/S4Vectors_defines.h:18,
                 from /tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/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-3.19-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-3.19-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 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-3.19-bioc/R/lib -lR
installing to /tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/00LOCK-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)
* 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/RtmpLl4NmO/RLIBS_272a344e7359f1/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 ‘hgu95av2cdf’
* removing ‘/tmp/RtmpLl4NmO/RLIBS_272a344e7359f1/hgu95av2cdf’
Warning in install.packages(cdfname, lib = lib, repos = repositories(),  :
  installation of package ‘hgu95av2cdf’ had non-zero exit status

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

Error: processing vignette 'farms.Rnw' failed with diagnostics:
 chunk 3 
Error in getCdfInfo(object) : 
  Could not obtain CDF environment, problems encountered:
Specified environment does not contain HG_U95Av2
Library - package hgu95av2cdf not installed
Library - package hgu95av2cdf not installed

--- failed re-building ‘farms.Rnw’

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

Error: Vignette re-building failed.
Execution halted

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

Status: 1 ERROR, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/farms.Rcheck/00check.log’
for details.


Installation output

farms.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL farms
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘farms’ ...
** using staged installation
** R
** data
** 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
Warning in fun(libname, pkgname) :
  Package 'farms' is deprecated and will be removed from Bioconductor
  version 3.20
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'farms' is deprecated and will be removed from Bioconductor
  version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (farms)

Tests output


Example timings

farms.Rcheck/farms-Ex.timings

nameusersystemelapsed
INI_Calls-class0.1300.0160.146
INIcalls-methods0.1430.0000.143
expFarms0.0190.0000.020
generateExprVal.method.farms0.0030.0000.004
getI_Eset-methods0.0290.0020.032
getI_ProbeSets-methods0.0340.0010.036
getNI_Eset-methods0.0290.0000.029
getNI_ProbeSets-methods0.0250.0040.030
lFarms0.0300.0000.029
plot-methods0.0310.0020.033
qFarms0.0170.0020.019
summary-methods0.0310.0000.031