##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:miaViz.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings miaViz_1.11.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/miaViz.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘miaViz/DESCRIPTION’ ... OK
* this is package ‘miaViz’ version ‘1.11.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘miaViz’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.add_signif_to_vector_labels : <anonymous>: no visible global function
  definition for ‘italic’
.clean_tree_data: no visible global function definition for ‘all_of’
.get_prevalence_plot_matrix: no visible binding for global variable
  ‘ID’
.rda_plotter: no visible binding for global variable ‘color’
Undefined global functions or variables:
  ID all_of color italic
* checking Rd files ... NOTE
checkRd: (-1) plotAbundanceDensity.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotAbundanceDensity.Rd:33-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotAbundanceDensity.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotAbundanceDensity.Rd:40-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotAbundanceDensity.Rd:43-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotAbundanceDensity.Rd:46-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotAbundanceDensity.Rd:49-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotAbundanceDensity.Rd:52-53: Lost braces in \itemize; meant \describe ?
* 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
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
plotTree             76.151  0.471  76.807
plotDMN              28.790  0.068  28.921
plotAbundanceDensity 12.437  0.263  18.438
plotAbundance        11.377  0.243  11.643
plotPrevalence       11.452  0.100  11.602
plotCCA               8.433  0.036   8.830
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/miaViz.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL miaViz
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library’
* installing *source* package ‘miaViz’ ...
** using staged installation
** R
** data
** 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 (miaViz)

R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(miaViz)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
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: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
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")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

Loading required package: TreeSummarizedExperiment
Loading required package: SingleCellExperiment
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: mia
Loading required package: MultiAssayExperiment
Loading required package: ggplot2
Loading required package: ggraph
> 
> test_check("miaViz")
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* installing *source* package ‘credentials’ ...
** package ‘credentials’ 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 (credentials)
* installing *source* package ‘zip’ ...
** package ‘zip’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
gcc -g -O2  -Wall miniz.c zip.c unixutils.c tools/cmdzip.c -o tools/cmdzip
gcc -g -O2  -Wall miniz.c zip.c unixutils.c tools/cmdunzip.c -o tools/cmdunzip
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c miniz.c -o miniz.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c rzip.c -o rzip.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c zip.c -o zip.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c unixutils.c -o unixutils.o
gcc -shared -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -L/usr/local/lib -o zip.so init.o miniz.o rzip.o zip.o unixutils.o -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -lR
installing via 'install.libs.R' to /home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/00LOCK-zip/00new/zip
** 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 (zip)
* installing *source* package ‘gitcreds’ ...
** package ‘gitcreds’ 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
** 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 (gitcreds)
* installing *source* package ‘httr2’ ...
** package ‘httr2’ 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 (httr2)
* installing *source* package ‘ini’ ...
** package ‘ini’ 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 (ini)
* installing *source* package ‘xtable’ ...
** package ‘xtable’ successfully unpacked and MD5 sums checked
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (xtable)
* installing *source* package ‘sourcetools’ ...
** package ‘sourcetools’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
using C++ compiler: ‘g++ (GCC) 10.3.1’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I../inst/include  -I/usr/local/include    -fPIC  -g -O2  -Wall  -c Reader.cpp -o Reader.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I../inst/include  -I/usr/local/include    -fPIC  -g -O2  -Wall  -c Tokenizer.cpp -o Tokenizer.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I../inst/include  -I/usr/local/include    -fPIC  -g -O2  -Wall -c sourcetools-init.c -o sourcetools-init.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -L/usr/local/lib -o sourcetools.so Reader.o Tokenizer.o sourcetools-init.o -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -lR
installing to /home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/00LOCK-sourcetools/00new/sourcetools/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 (sourcetools)
* installing *source* package ‘later’ ...
** package ‘later’ successfully unpacked and MD5 sums checked
** using staged installation
Running configure script
-latomic linker flag not needed.
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
using C++ compiler: ‘g++ (GCC) 10.3.1’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c callback_registry.cpp -o callback_registry.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c debug.cpp -o debug.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c init.c -o init.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c later.cpp -o later.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c later_posix.cpp -o later_posix.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c later_win32.cpp -o later_win32.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c timer_posix.cpp -o timer_posix.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c timestamp_unix.cpp -o timestamp_unix.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c timestamp_win32.cpp -o timestamp_win32.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c tinycthread.c -o tinycthread.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -L/usr/local/lib -o later.so RcppExports.o callback_registry.o debug.o init.o later.o later_posix.o later_win32.o timer_posix.o timestamp_unix.o timestamp_win32.o tinycthread.o -pthread -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -lR
installing to /home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/00LOCK-later/00new/later/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 (later)
* installing *source* package ‘clipr’ ...
** package ‘clipr’ 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
** 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 (clipr)
* installing *source* package ‘rstudioapi’ ...
** package ‘rstudioapi’ 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 (rstudioapi)
* installing *source* package ‘whisker’ ...
** package ‘whisker’ 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 (whisker)
* installing *source* package ‘downlit’ ...
** package ‘downlit’ 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 (downlit)
* installing *source* package ‘xml2’ ...
** package ‘xml2’ successfully unpacked and MD5 sums checked
** using staged installation
Found pkg-config cflags and libs!
Using PKG_CFLAGS=-I/usr/include/libxml2
Using PKG_LIBS=-lxml2 -lz -llzma -lm
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
using C++ compiler: ‘g++ (GCC) 10.3.1’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall  -c connection.cpp -o connection.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0  -I/usr/local/include    -fPIC  -g -O2  -Wall -c init.c -o init.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall  -c xml2_doc.cpp -o xml2_doc.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall  -c xml2_init.cpp -o xml2_init.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall  -c xml2_namespace.cpp -o xml2_namespace.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall  -c xml2_node.cpp -o xml2_node.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall  -c xml2_output.cpp -o xml2_output.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall  -c xml2_schema.cpp -o xml2_schema.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall  -c xml2_url.cpp -o xml2_url.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall  -c xml2_xpath.cpp -o xml2_xpath.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -L/usr/local/lib -o xml2.so connection.o init.o xml2_doc.o xml2_init.o xml2_namespace.o xml2_node.o xml2_output.o xml2_schema.o xml2_url.o xml2_xpath.o -lxml2 -lz -llzma -lm -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -lR
installing to /home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/00LOCK-xml2/00new/xml2/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 (xml2)
* installing *source* package ‘htmlwidgets’ ...
** package ‘htmlwidgets’ 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
** 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 (htmlwidgets)
* installing *source* package ‘prettyunits’ ...
** package ‘prettyunits’ 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 (prettyunits)
* installing *source* package ‘xopen’ ...
** package ‘xopen’ 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 (xopen)
* installing *source* package ‘brew’ ...
** package ‘brew’ 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 (brew)
* installing *source* package ‘commonmark’ ...
** package ‘commonmark’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
rm -f cmark/cmark.o cmark/node.o cmark/iterator.o cmark/blocks.o cmark/inlines.o cmark/scanners.o cmark/utf8.o cmark/buffer.o cmark/references.o cmark/render.o cmark/man.o cmark/xml.o cmark/html.o cmark/commonmark.o cmark/latex.o cmark/houdini_href_e.o cmark/houdini_html_e.o cmark/houdini_html_u.o cmark/cmark_ctype.o cmark/arena.o cmark/linked_list.o cmark/plugin.o cmark/registry.o cmark/syntax_extension.o cmark/plaintext.o cmark/footnotes.o cmark/map.o extensions/autolink.o extensions/core-extensions.o extensions/ext_scanners.o extensions/strikethrough.o extensions/table.o extensions/tagfilter.o extensions/tasklist.o extensions.o init.o wrapper.o commonmark.so cmark/libstatcmark.a
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c extensions.c -o extensions.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c wrapper.c -o wrapper.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c cmark/cmark.c -o cmark/cmark.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c cmark/node.c -o cmark/node.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c cmark/iterator.c -o cmark/iterator.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c cmark/blocks.c -o cmark/blocks.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c cmark/inlines.c -o cmark/inlines.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c cmark/scanners.c -o cmark/scanners.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c cmark/utf8.c -o cmark/utf8.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c cmark/buffer.c -o cmark/buffer.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c cmark/references.c -o cmark/references.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c cmark/render.c -o cmark/render.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c cmark/man.c -o cmark/man.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c cmark/xml.c -o cmark/xml.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c cmark/html.c -o cmark/html.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c cmark/commonmark.c -o cmark/commonmark.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c cmark/latex.c -o cmark/latex.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c cmark/houdini_href_e.c -o cmark/houdini_href_e.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c cmark/houdini_html_e.c -o cmark/houdini_html_e.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c cmark/houdini_html_u.c -o cmark/houdini_html_u.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c cmark/cmark_ctype.c -o cmark/cmark_ctype.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c cmark/arena.c -o cmark/arena.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c cmark/linked_list.c -o cmark/linked_list.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c cmark/plugin.c -o cmark/plugin.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c cmark/registry.c -o cmark/registry.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c cmark/syntax_extension.c -o cmark/syntax_extension.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c cmark/plaintext.c -o cmark/plaintext.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c cmark/footnotes.c -o cmark/footnotes.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c cmark/map.c -o cmark/map.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c extensions/autolink.c -o extensions/autolink.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c extensions/core-extensions.c -o extensions/core-extensions.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c extensions/ext_scanners.c -o extensions/ext_scanners.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c extensions/strikethrough.c -o extensions/strikethrough.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c extensions/table.c -o extensions/table.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c extensions/tagfilter.c -o extensions/tagfilter.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Icmark -I. -DCMARK_GFM_STATIC_DEFINE -DCMARK_GFM_EXTENSIONS_STATIC_DEFINE -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c extensions/tasklist.c -o extensions/tasklist.o
ar rcs cmark/libstatcmark.a cmark/cmark.o cmark/node.o cmark/iterator.o cmark/blocks.o cmark/inlines.o cmark/scanners.o cmark/utf8.o cmark/buffer.o cmark/references.o cmark/render.o cmark/man.o cmark/xml.o cmark/html.o cmark/commonmark.o cmark/latex.o cmark/houdini_href_e.o cmark/houdini_html_e.o cmark/houdini_html_u.o cmark/cmark_ctype.o cmark/arena.o cmark/linked_list.o cmark/plugin.o cmark/registry.o cmark/syntax_extension.o cmark/plaintext.o cmark/footnotes.o cmark/map.o extensions/autolink.o extensions/core-extensions.o extensions/ext_scanners.o extensions/strikethrough.o extensions/table.o extensions/tagfilter.o extensions/tasklist.o
gcc -shared -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -L/usr/local/lib -o commonmark.so extensions.o init.o wrapper.o -Lcmark -lstatcmark -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -lR
installing to /home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/00LOCK-commonmark/00new/commonmark/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 (commonmark)
* installing *source* package ‘ellipsis’ ...
** package ‘ellipsis’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c dots.c -o dots.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c init.c -o init.o
gcc -shared -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -L/usr/local/lib -o ellipsis.so dots.o init.o -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -lR
installing to /home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/00LOCK-ellipsis/00new/ellipsis/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 (ellipsis)
* installing *source* package ‘remotes’ ...
** package ‘remotes’ 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
** 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 (remotes)
* installing *source* package ‘sessioninfo’ ...
** package ‘sessioninfo’ 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 (sessioninfo)
* installing *source* package ‘promises’ ...
** package ‘promises’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG  -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/later/include' -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG  -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/later/include' -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c promise_task.cpp -o promise_task.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -L/usr/local/lib -o promises.so RcppExports.o promise_task.o -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -lR
installing to /home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/00LOCK-promises/00new/promises/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 (promises)
* installing *source* package ‘gert’ ...
** package ‘gert’ successfully unpacked and MD5 sums checked
** using staged installation
Found pkg-config cflags and libs!
Using PKG_CFLAGS=
Using PKG_LIBS=-lgit2 
Configuration OK!
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
rm -f gert.so branch.o clone.o commit.o config.o conflicts.o files.o ignore.o init.o merge.o rebase.o stash.o submodules.o tag.o utils.o version.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c branch.c -o branch.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c clone.c -o clone.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c commit.c -o commit.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c config.c -o config.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c conflicts.c -o conflicts.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c files.c -o files.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c ignore.c -o ignore.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c merge.c -o merge.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c rebase.c -o rebase.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c stash.c -o stash.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c submodules.c -o submodules.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c tag.c -o tag.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c utils.c -o utils.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fPIC  -g -O2  -Wall -c version.c -o version.o
gcc -shared -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -L/usr/local/lib -o gert.so branch.o clone.o commit.o config.o conflicts.o files.o ignore.o init.o merge.o rebase.o stash.o submodules.o tag.o utils.o version.o -lgit2 -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -lR
installing to /home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/00LOCK-gert/00new/gert/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 (gert)
* installing *source* package ‘gh’ ...
** package ‘gh’ 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
** 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 (gh)
* installing *source* package ‘pkgdown’ ...
** package ‘pkgdown’ 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 (pkgdown)
* installing *source* package ‘profvis’ ...
** package ‘profvis’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c pause.c -o pause.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c profvis-init.c -o profvis-init.o
gcc -shared -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -L/usr/local/lib -o profvis.so pause.o profvis-init.o -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -lR
installing to /home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/00LOCK-profvis/00new/profvis/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 (profvis)
* installing *source* package ‘rcmdcheck’ ...
** package ‘rcmdcheck’ 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 (rcmdcheck)
* installing *source* package ‘roxygen2’ ...
** package ‘roxygen2’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG  -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/cpp11/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c cpp11.cpp -o cpp11.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG  -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/cpp11/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c escapeExamples.cpp -o escapeExamples.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG  -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/cpp11/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c isComplete.cpp -o isComplete.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG  -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/cpp11/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c leadingSpaces.cpp -o leadingSpaces.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG  -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/cpp11/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c parser2.cpp -o parser2.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG  -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/cpp11/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c wrapUsage.cpp -o wrapUsage.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -L/usr/local/lib -o roxygen2.so cpp11.o escapeExamples.o isComplete.o leadingSpaces.o parser2.o wrapUsage.o -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -lR
installing to /home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/00LOCK-roxygen2/00new/roxygen2/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 (roxygen2)
* installing *source* package ‘rversions’ ...
** package ‘rversions’ 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 (rversions)
* installing *source* package ‘urlchecker’ ...
** package ‘urlchecker’ 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 (urlchecker)
* installing *source* package ‘httpuv’ ...
** package ‘httpuv’ successfully unpacked and MD5 sums checked
** using staged installation
** Using bundled copy of libuv
** PKG_CFLAGS=-Ilibuv/include
** PKG_LIBS=./libuv/.libs/libuv.a
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
using C++ compiler: ‘g++ (GCC) 10.3.1’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/later/include' -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fPIC  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/later/include' -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fPIC  -g -O2  -Wall  -c callback.cpp -o callback.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/later/include' -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fPIC  -g -O2  -Wall  -c callbackqueue.cpp -o callbackqueue.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/later/include' -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fPIC  -g -O2  -Wall  -c filedatasource-unix.cpp -o filedatasource-unix.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/later/include' -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fPIC  -g -O2  -Wall  -c filedatasource-win.cpp -o filedatasource-win.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/later/include' -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fPIC  -g -O2  -Wall  -c fs.cpp -o fs.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/later/include' -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fPIC  -g -O2  -Wall  -c gzipdatasource.cpp -o gzipdatasource.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/later/include' -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fPIC  -g -O2  -Wall  -c http.cpp -o http.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/later/include' -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fPIC  -g -O2  -Wall  -c httprequest.cpp -o httprequest.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/later/include' -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fPIC  -g -O2  -Wall  -c httpresponse.cpp -o httpresponse.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/later/include' -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fPIC  -g -O2  -Wall  -c httpuv.cpp -o httpuv.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/later/include' -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fPIC  -g -O2  -Wall -c md5.c -o md5.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/later/include' -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fPIC  -g -O2  -Wall  -c mime.cpp -o mime.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/later/include' -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fPIC  -g -O2  -Wall  -c socket.cpp -o socket.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/later/include' -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fPIC  -g -O2  -Wall  -c staticpath.cpp -o staticpath.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/later/include' -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fPIC  -g -O2  -Wall  -c thread.cpp -o thread.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/later/include' -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fPIC  -g -O2  -Wall  -c timegm.cpp -o timegm.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/later/include' -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fPIC  -g -O2  -Wall  -c utils.cpp -o utils.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/later/include' -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fPIC  -g -O2  -Wall  -c uvutil.cpp -o uvutil.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/later/include' -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fPIC  -g -O2  -Wall  -c webapplication.cpp -o webapplication.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/later/include' -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fPIC  -g -O2  -Wall  -c websockets-base.cpp -o websockets-base.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/later/include' -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fPIC  -g -O2  -Wall  -c websockets-hixie76.cpp -o websockets-hixie76.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/later/include' -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fPIC  -g -O2  -Wall  -c websockets-hybi03.cpp -o websockets-hybi03.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/later/include' -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fPIC  -g -O2  -Wall  -c websockets-ietf.cpp -o websockets-ietf.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/later/include' -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fPIC  -g -O2  -Wall  -c websockets.cpp -o websockets.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/later/include' -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fPIC  -g -O2  -Wall  -c winutils.cpp -o winutils.o
cp -p -f libuv/m4/lt_obsolete.m4 libuv/m4/lt~obsolete.m4
cd libuv; \
if ! command -v automake >/dev/null 2>&1 ; then \
	echo "automake not found. Touching files so configure will not try to run automake."; \
	touch aclocal.m4; \
	touch -r aclocal.m4 configure Makefile.in; \
else \
	echo "automake found. Running autoupdate and autogen.sh."; \
	autoupdate; \
	sh autogen.sh; \
fi; \
chmod +x configure; \
CC="gcc" CFLAGS="-g -O2  -Wall -fPIC -fvisibility=hidden -DNDEBUG" CPPFLAGS="-I/usr/local/include" AR="ar" RANLIB="ranlib" LDFLAGS="-L/usr/local/lib" ./configure "--quiet"
automake found. Running autoupdate and autogen.sh.
+ libtoolize --copy
autogen.sh: line 43: libtoolize: command not found
make --directory=libuv \
	HAVE_DTRACE=0
make[1]: Entering directory '/home/biocbuild/tmp/RtmpUc3mAS/R.INSTALL1ea7be6c4b7f15/httpuv/src/libuv'
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh '/home/biocbuild/tmp/RtmpUc3mAS/R.INSTALL1ea7be6c4b7f15/httpuv/src/libuv/missing' aclocal-1.16 -I m4
 cd . && /bin/sh /home/biocbuild/tmp/RtmpUc3mAS/R.INSTALL1ea7be6c4b7f15/httpuv/src/libuv/missing automake-1.16 --foreign
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh '/home/biocbuild/tmp/RtmpUc3mAS/R.INSTALL1ea7be6c4b7f15/httpuv/src/libuv/missing' autoconf
configure.ac:46: warning: $as_echo is obsolete; use AS_ECHO(["message"]) instead
lib/m4sugar/m4sh.m4:692: _AS_IF_ELSE is expanded from...
lib/m4sugar/m4sh.m4:699: AS_IF is expanded from...
./lib/autoconf/general.m4:2249: AC_CACHE_VAL is expanded from...
./lib/autoconf/general.m4:2270: AC_CACHE_CHECK is expanded from...
m4/ax_pthread.m4:88: AX_PTHREAD is expanded from...
configure.ac:46: the top level
/bin/sh ./config.status --recheck
running CONFIG_SHELL=/bin/sh /bin/sh ./configure CC=gcc CFLAGS=-g -O2  -Wall -fPIC -fvisibility=hidden -DNDEBUG LDFLAGS=-L/usr/local/lib CPPFLAGS=-I/usr/local/include --no-create --no-recursion
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking build system type... aarch64-unknown-linux-gnu
checking host system type... aarch64-unknown-linux-gnu
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking whether gcc understands -c and -o together... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of gcc... gcc3
checking for gcc way to treat warnings as errors... -Werror
checking if gcc supports __attribute__(( visibility("default") ))... yes
checking if gcc supports -fvisibility=hidden... yes
checking if gcc supports -fno-strict-aliasing flag... yes
checking if gcc supports -g flag... yes
checking if gcc supports -std=gnu89 flag... yes
checking if gcc supports -Wall flag... yes
checking if gcc supports -Wextra flag... yes
checking if gcc supports -Wno-long-long flag... yes
checking if gcc supports -Wno-unused-parameter flag... yes
checking if gcc supports -Wno-declaration-after-statement flag... yes
checking if gcc supports -Wstrict-prototypes flag... yes
checking for ar... ar
checking the archiver (ar) interface... ar
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert aarch64-unknown-linux-gnu file names to aarch64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert aarch64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /usr/bin/dd
checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking whether make supports nested variables... (cached) yes
checking how to run the C preprocessor... gcc -E
checking whether gcc is Clang... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking whether more special flags are required for pthreads... no
checking for PTHREAD_PRIO_INHERIT... yes
checking for library containing dlopen... none required
checking for library containing kstat_lookup... no
checking for library containing gethostbyname... none required
checking for library containing perfstat_cpu... no
checking for library containing clock_gettime... none required
checking for library containing sendfile... none required
checking for library containing socket... none required
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for sys/ahafs_evProds.h... no
checking that generated files are newer than configure... done
configure: creating ./config.status
 /bin/sh ./config.status
config.status: creating Makefile
config.status: creating libuv.pc
config.status: executing depfiles commands
config.status: executing libtool commands
  CC       src/libuv_la-fs-poll.lo
  CC       src/libuv_la-idna.lo
  CC       src/libuv_la-inet.lo
  CC       src/libuv_la-random.lo
  CC       src/libuv_la-strscpy.lo
  CC       src/libuv_la-threadpool.lo
  CC       src/libuv_la-timer.lo
  CC       src/libuv_la-uv-data-getter-setters.lo
  CC       src/libuv_la-uv-common.lo
  CC       src/libuv_la-version.lo
  CC       src/unix/libuv_la-async.lo
  CC       src/unix/libuv_la-core.lo
  CC       src/unix/libuv_la-dl.lo
  CC       src/unix/libuv_la-fs.lo
  CC       src/unix/libuv_la-getaddrinfo.lo
  CC       src/unix/libuv_la-getnameinfo.lo
  CC       src/unix/libuv_la-loop-watcher.lo
  CC       src/unix/libuv_la-loop.lo
  CC       src/unix/libuv_la-pipe.lo
  CC       src/unix/libuv_la-poll.lo
  CC       src/unix/libuv_la-process.lo
  CC       src/unix/libuv_la-random-devurandom.lo
  CC       src/unix/libuv_la-signal.lo
  CC       src/unix/libuv_la-stream.lo
  CC       src/unix/libuv_la-tcp.lo
  CC       src/unix/libuv_la-thread.lo
src/unix/thread.c: In function ‘uv__thread_stack_size’:
src/unix/thread.c:195:24: warning: comparison of integer expressions of different signedness: ‘rlim_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare]
  195 |       if (lim.rlim_cur >= PTHREAD_STACK_MIN)
      |                        ^~
src/unix/thread.c: In function ‘uv_thread_create_ex’:
src/unix/thread.c:243:20: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare]
  243 |     if (stack_size < PTHREAD_STACK_MIN)
      |                    ^
  CC       src/unix/libuv_la-tty.lo
  CC       src/unix/libuv_la-udp.lo
  CC       src/unix/libuv_la-linux-core.lo
  CC       src/unix/libuv_la-linux-inotify.lo
  CC       src/unix/libuv_la-linux-syscalls.lo
  CC       src/unix/libuv_la-procfs-exepath.lo
  CC       src/unix/libuv_la-proctitle.lo
  CC       src/unix/libuv_la-random-getrandom.lo
  CC       src/unix/libuv_la-random-sysctl-linux.lo
  CC       src/unix/libuv_la-epoll.lo
  CCLD     libuv.la
make[1]: Leaving directory '/home/biocbuild/tmp/RtmpUc3mAS/R.INSTALL1ea7be6c4b7f15/httpuv/src/libuv'
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/later/include' -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fPIC  -g -O2  -Wall -c http-parser/http_parser.c -o http-parser/http_parser.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/later/include' -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fPIC  -g -O2  -Wall -c sha1/sha1.c -o sha1/sha1.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/later/include' -I'/home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fPIC  -g -O2  -Wall  -c base64/base64.cpp -o base64/base64.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -L/usr/local/lib -o httpuv.so RcppExports.o callback.o callbackqueue.o filedatasource-unix.o filedatasource-win.o fs.o gzipdatasource.o http.o httprequest.o httpresponse.o httpuv.o md5.o mime.o socket.o staticpath.o thread.o timegm.o utils.o uvutil.o webapplication.o websockets-base.o websockets-hixie76.o websockets-hybi03.o websockets-ietf.o websockets.o winutils.o ./libuv/.libs/libuv.a ./http-parser/http_parser.o ./sha1/sha1.o ./base64/base64.o -pthread -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -lR
installing to /home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/00LOCK-httpuv/00new/httpuv/libs
** R
** demo
** 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 (httpuv)
* installing *source* package ‘usethis’ ...
** package ‘usethis’ 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
** 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 (usethis)
* installing *source* package ‘shiny’ ...
** package ‘shiny’ 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
** 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 (shiny)
* installing *source* package ‘miniUI’ ...
** package ‘miniUI’ 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 (miniUI)
* installing *source* package ‘devtools’ ...
** package ‘devtools’ 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 (devtools)

The downloaded source packages are in
	'/home/biocbuild/tmp/RtmpNrn79G/downloaded_packages'
bitops (NA -> 1.0-7    ) [CRAN]
RCurl  (NA -> 1.98-1.14) [CRAN]
trying URL 'https://cloud.r-project.org/src/contrib/bitops_1.0-7.tar.gz'
Content type 'application/x-gzip' length 10809 bytes (10 KB)
==================================================
downloaded 10 KB

trying URL 'https://cloud.r-project.org/src/contrib/RCurl_1.98-1.14.tar.gz'
Content type 'application/x-gzip' length 731307 bytes (714 KB)
==================================================
downloaded 714 KB

* installing *source* package ‘bitops’ ...
** package ‘bitops’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c bit-ops.c -o bit-ops.o
bit-ops.c: In function ‘bitShiftL’:
bit-ops.c:125:66: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses]
  125 |   else *(xaAb++)=(double) (_2_UINT_(xa[i]) __OP__ I_2_UINT(xb[j] & 31 ) ) ; \
      |                                                                  ^
bit-ops.c:6:50: note: in definition of macro ‘I_2_UINT’
    6 | #define I_2_UINT(I)   (unsigned int) ((I) < 0 ? (I + UINT_MAX +1) : (I))
      |                                                  ^
bit-ops.c:145:5: note: in expansion of macro ‘bitshift_BODY’
  145 |     bitshift_BODY( << );
      |     ^~~~~~~~~~~~~
bit-ops.c:136:66: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses]
  136 |   else *(xaAb++)=(double) (_2_UINT_(xa[j]) __OP__ I_2_UINT(xb[i] & 31 )) ; \
      |                                                                  ^
bit-ops.c:6:50: note: in definition of macro ‘I_2_UINT’
    6 | #define I_2_UINT(I)   (unsigned int) ((I) < 0 ? (I + UINT_MAX +1) : (I))
      |                                                  ^
bit-ops.c:145:5: note: in expansion of macro ‘bitshift_BODY’
  145 |     bitshift_BODY( << );
      |     ^~~~~~~~~~~~~
bit-ops.c: In function ‘bitShiftR’:
bit-ops.c:125:66: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses]
  125 |   else *(xaAb++)=(double) (_2_UINT_(xa[i]) __OP__ I_2_UINT(xb[j] & 31 ) ) ; \
      |                                                                  ^
bit-ops.c:6:50: note: in definition of macro ‘I_2_UINT’
    6 | #define I_2_UINT(I)   (unsigned int) ((I) < 0 ? (I + UINT_MAX +1) : (I))
      |                                                  ^
bit-ops.c:149:5: note: in expansion of macro ‘bitshift_BODY’
  149 |     bitshift_BODY( >> );
      |     ^~~~~~~~~~~~~
bit-ops.c:136:66: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses]
  136 |   else *(xaAb++)=(double) (_2_UINT_(xa[j]) __OP__ I_2_UINT(xb[i] & 31 )) ; \
      |                                                                  ^
bit-ops.c:6:50: note: in definition of macro ‘I_2_UINT’
    6 | #define I_2_UINT(I)   (unsigned int) ((I) < 0 ? (I + UINT_MAX +1) : (I))
      |                                                  ^
bit-ops.c:149:5: note: in expansion of macro ‘bitshift_BODY’
  149 |     bitshift_BODY( >> );
      |     ^~~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c cksum.c -o cksum.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c init.c -o init.o
gcc -shared -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -L/usr/local/lib -o bitops.so bit-ops.o cksum.o init.o -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -lR
installing to /home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/00LOCK-bitops/00new/bitops/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (bitops)
* installing *source* package ‘RCurl’ ...
** package ‘RCurl’ successfully unpacked and MD5 sums checked
** using staged installation
checking for curl-config... /usr/bin/curl-config
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking how to run the C preprocessor... gcc -E
Version has a libidn field
Version has CURLOPT_URL
Version has CURLINFO_EFFECTIVE_URL
Version has CURLINFO_RESPONSE_CODE
Version has CURLINFO_TOTAL_TIME
Version has CURLINFO_NAMELOOKUP_TIME
Version has CURLINFO_CONNECT_TIME
Version has CURLINFO_PRETRANSFER_TIME
Version has CURLINFO_SIZE_UPLOAD
Version has CURLINFO_SIZE_DOWNLOAD
Version has CURLINFO_SPEED_DOWNLOAD
Version has CURLINFO_SPEED_UPLOAD
Version has CURLINFO_HEADER_SIZE
Version has CURLINFO_REQUEST_SIZE
Version has CURLINFO_SSL_VERIFYRESULT
Version has CURLINFO_FILETIME
Version has CURLINFO_CONTENT_LENGTH_DOWNLOAD
Version has CURLINFO_CONTENT_LENGTH_UPLOAD
Version has CURLINFO_STARTTRANSFER_TIME
Version has CURLINFO_CONTENT_TYPE
Version has CURLINFO_REDIRECT_TIME
Version has CURLINFO_REDIRECT_COUNT
Version has CURLINFO_PRIVATE
Version has CURLINFO_HTTP_CONNECTCODE
Version has CURLINFO_HTTPAUTH_AVAIL
Version has CURLINFO_PROXYAUTH_AVAIL
Version has CURLINFO_OS_ERRNO
Version has CURLINFO_NUM_CONNECTS
Version has CURLINFO_SSL_ENGINES
Version has CURLINFO_COOKIELIST
Version has CURLINFO_LASTSOCKET
Version has CURLINFO_FTP_ENTRY_PATH
Version has CURLINFO_REDIRECT_URL
Version has CURLINFO_PRIMARY_IP
Version has CURLINFO_APPCONNECT_TIME
Version has CURLINFO_CERTINFO
Version has CURLINFO_CONDITION_UNMET
Version has CURLOPT_WRITEDATA
Version has CURLOPT_KEYPASSWD
Version has CURLOPT_DIRLISTONLY
Version has CURLOPT_APPEND
Version has CURLOPT_KRBLEVEL
Version has CURLOPT_USE_SSL
Version has CURLOPT_TIMEOUT_MS
Version has CURLOPT_CONNECTTIMEOUT_MS
Version has CURLOPT_HTTP_TRANSFER_DECODING
Version has CURLOPT_HTTP_CONTENT_DECODING
Version has CURLOPT_NEW_FILE_PERMS
Version has CURLOPT_NEW_DIRECTORY_PERMS
Version has CURLOPT_POSTREDIR
Version has CURLOPT_OPENSOCKETFUNCTION
Version has CURLOPT_OPENSOCKETDATA
Version has CURLOPT_COPYPOSTFIELDS
Version has CURLOPT_PROXY_TRANSFER_MODE
Version has CURLOPT_SEEKFUNCTION
Version has CURLOPT_SEEKDATA
Version has CURLOPT_CRLFILE
Version has CURLOPT_ISSUERCERT
Version has CURLOPT_ADDRESS_SCOPE
Version has CURLOPT_CERTINFO
Version has CURLOPT_USERNAME
Version has CURLOPT_PASSWORD
Version has CURLOPT_PROXYUSERNAME
Version has CURLOPT_PROXYPASSWORD
Version has CURLOPT_SSH_HOST_PUBLIC_KEY_MD5
Version has CURLOPT_NOPROXY
Version has CURLOPT_TFTP_BLKSIZE
Version has CURLOPT_SOCKS5_GSSAPI_SERVICE
Version has CURLOPT_SOCKS5_GSSAPI_NEC
Version has CURLOPT_PROTOCOLS
Version has CURLOPT_REDIR_PROTOCOLS
Version has CURLOPT_SSH_AUTH_TYPES
Version has CURLOPT_SSH_PUBLIC_KEYFILE
Version has CURLOPT_SSH_PRIVATE_KEYFILE
Version has CURLOPT_FTP_SSL_CCC
Version has CURLOPT_COOKIELIST
Version has CURLOPT_IGNORE_CONTENT_LENGTH
Version has CURLOPT_FTP_SKIP_PASV_IP
Version has CURLOPT_FTP_FILEMETHOD
Version has CURLOPT_LOCALPORT
Version has CURLOPT_LOCALPORTRANGE
Version has CURLOPT_CONNECT_ONLY
Version has CURLOPT_CONV_FROM_NETWORK_FUNCTION
Version has CURLOPT_CONV_TO_NETWORK_FUNCTION
Version has CURLOPT_CONV_FROM_UTF8_FUNCTION
Version has CURLOPT_MAX_SEND_SPEED_LARGE
Version has CURLOPT_MAX_RECV_SPEED_LARGE
Version has CURLOPT_FTP_ALTERNATIVE_TO_USER
Version has CURLOPT_SOCKOPTFUNCTION
Version has CURLOPT_SOCKOPTDATA
Version has CURLOPT_SSL_SESSIONID_CACHE
libcurl version: libcurl 7.79.1
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include    -fPIC  -g -O2  -Wall -c base64.c -o base64.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include    -fPIC  -g -O2  -Wall -c curl.c -o curl.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include    -fPIC  -g -O2  -Wall -c curlInit.c -o curlInit.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include    -fPIC  -g -O2  -Wall -c curl_base64.c -o curl_base64.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include    -fPIC  -g -O2  -Wall -c enums.c -o enums.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include    -fPIC  -g -O2  -Wall -c json.c -o json.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include    -fPIC  -g -O2  -Wall -c memoryManagement.c -o memoryManagement.o
gcc -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include    -fPIC  -g -O2  -Wall -c myUTF8.c -o myUTF8.o
gcc -shared -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -L/usr/local/lib -o RCurl.so base64.o curl.o curlInit.o curl_base64.o enums.o json.o memoryManagement.o myUTF8.o -lcurl -lxml2 -lz -llzma -lm -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -lR
installing to /home/biocbuild/tmp/RtmpD0PNTZ/RLIBS_1dfb6f60f66dbb/00LOCK-RCurl/00new/RCurl/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RCurl)

The downloaded source packages are in
	'/home/biocbuild/tmp/RtmpNrn79G/downloaded_packages'
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/home/biocbuild/tmp/RtmpNrn79G/remotes1e4d2426b3b755/microbiome-miaTime-9fe9771/DESCRIPTION’ ... OK
* preparing ‘miaTime’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘miaTime_0.1.21.tar.gz’

* installing *source* package ‘miaTime’ ...
** using staged installation
** R
** data
** 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 (miaTime)
[ FAIL 0 | WARN 7 | SKIP 0 | PASS 215 ]

[ FAIL 0 | WARN 7 | SKIP 0 | PASS 215 ]
> 
> proc.time()
   user  system elapsed 
659.100  48.155 725.010