Multiple platform build/check report for BioC 3.19 - CHECK results for miaViz on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"	4708
palomino3	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences"	4446
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"	4471
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences"	4426
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.

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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
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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")
trying URL 'https://cloud.r-project.org/src/contrib/credentials_2.0.1.tar.gz'
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trying URL 'https://cloud.r-project.org/src/contrib/zip_2.3.1.tar.gz'
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trying URL 'https://cloud.r-project.org/src/contrib/gitcreds_0.1.2.tar.gz'
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trying URL 'https://cloud.r-project.org/src/contrib/httr2_1.0.0.tar.gz'
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downloaded 207 KB

trying URL 'https://cloud.r-project.org/src/contrib/ini_0.3.1.tar.gz'
Content type 'application/x-gzip' length 3488 bytes
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downloaded 3488 bytes

trying URL 'https://cloud.r-project.org/src/contrib/httpuv_1.6.15.tar.gz'
Content type 'application/x-gzip' length 1879369 bytes (1.8 MB)
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downloaded 1.8 MB

trying URL 'https://cloud.r-project.org/src/contrib/xtable_1.8-4.tar.gz'
Content type 'application/x-gzip' length 564589 bytes (551 KB)
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downloaded 551 KB

trying URL 'https://cloud.r-project.org/src/contrib/sourcetools_0.1.7-1.tar.gz'
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trying URL 'https://cloud.r-project.org/src/contrib/later_1.3.2.tar.gz'
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trying URL 'https://cloud.r-project.org/src/contrib/clipr_0.8.0.tar.gz'
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trying URL 'https://cloud.r-project.org/src/contrib/rstudioapi_0.16.0.tar.gz'
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trying URL 'https://cloud.r-project.org/src/contrib/whisker_0.4.1.tar.gz'
Content type 'application/x-gzip' length 28586 bytes (27 KB)
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trying URL 'https://cloud.r-project.org/src/contrib/shiny_1.8.1.tar.gz'
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trying URL 'https://cloud.r-project.org/src/contrib/downlit_0.4.3.tar.gz'
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trying URL 'https://cloud.r-project.org/src/contrib/xml2_1.3.6.tar.gz'
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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 (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
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/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c miniz.c -o miniz.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c rzip.c -o rzip.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c zip.c -o zip.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c unixutils.c -o unixutils.o
gcc -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o zip.so init.o miniz.o rzip.o zip.o unixutils.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing via 'install.libs.R' to /tmp/RtmpHWD2ve/RLIBS_ebf91d106758/00LOCK-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 (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include  -I/usr/local/include    -fpic  -g -O2  -Wall  -c Reader.cpp -o Reader.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include  -I/usr/local/include    -fpic  -g -O2  -Wall  -c Tokenizer.cpp -o Tokenizer.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/lib -L/usr/local/lib -o sourcetools.so Reader.o Tokenizer.o sourcetools-init.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpHWD2ve/RLIBS_ebf91d106758/00LOCK-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 (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/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/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c debug.cpp -o debug.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c later.cpp -o later.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/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/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/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/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/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/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/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/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c timestamp_win32.cpp -o timestamp_win32.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS  -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c tinycthread.c -o tinycthread.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpHWD2ve/RLIBS_ebf91d106758/00LOCK-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
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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 -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpHWD2ve/RLIBS_ebf91d106758/00LOCK-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 (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/lib -L/usr/local/lib -o commonmark.so extensions.o init.o wrapper.o -Lcmark -lstatcmark -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpHWD2ve/RLIBS_ebf91d106758/00LOCK-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 (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c dots.c -o dots.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o ellipsis.so dots.o init.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpHWD2ve/RLIBS_ebf91d106758/00LOCK-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++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/later/include' -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/later/include' -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/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/bbs-3.19-bioc/R/lib -L/usr/local/lib -o promises.so RcppExports.o promise_task.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpHWD2ve/RLIBS_ebf91d106758/00LOCK-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 OpenSSL3
Using static libgit2 for Linux x86_64
Using PKG_CFLAGS=-DSTATIC_LIBGIT2 -I/tmp/RtmpFfSwlB/R.INSTALLfc5ed12818295/gert/libgit2-1.4.2-x86_64_linux/include
Using PKG_LIBS=-L/tmp/RtmpFfSwlB/R.INSTALLfc5ed12818295/gert/libgit2-1.4.2-x86_64_linux/lib -lstatgit2 -lrt -lpthread -lstatssh2 -lstatssl -lstatcrypto -ldl
Configuration OK!
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
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/bbs-3.19-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpFfSwlB/R.INSTALLfc5ed12818295/gert/libgit2-1.4.2-x86_64_linux/include -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/bbs-3.19-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpFfSwlB/R.INSTALLfc5ed12818295/gert/libgit2-1.4.2-x86_64_linux/include -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/bbs-3.19-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpFfSwlB/R.INSTALLfc5ed12818295/gert/libgit2-1.4.2-x86_64_linux/include -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/bbs-3.19-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpFfSwlB/R.INSTALLfc5ed12818295/gert/libgit2-1.4.2-x86_64_linux/include -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/bbs-3.19-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpFfSwlB/R.INSTALLfc5ed12818295/gert/libgit2-1.4.2-x86_64_linux/include -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/bbs-3.19-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpFfSwlB/R.INSTALLfc5ed12818295/gert/libgit2-1.4.2-x86_64_linux/include -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/bbs-3.19-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpFfSwlB/R.INSTALLfc5ed12818295/gert/libgit2-1.4.2-x86_64_linux/include -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/bbs-3.19-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpFfSwlB/R.INSTALLfc5ed12818295/gert/libgit2-1.4.2-x86_64_linux/include -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/bbs-3.19-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpFfSwlB/R.INSTALLfc5ed12818295/gert/libgit2-1.4.2-x86_64_linux/include -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/bbs-3.19-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpFfSwlB/R.INSTALLfc5ed12818295/gert/libgit2-1.4.2-x86_64_linux/include -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/bbs-3.19-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpFfSwlB/R.INSTALLfc5ed12818295/gert/libgit2-1.4.2-x86_64_linux/include -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/bbs-3.19-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpFfSwlB/R.INSTALLfc5ed12818295/gert/libgit2-1.4.2-x86_64_linux/include -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/bbs-3.19-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpFfSwlB/R.INSTALLfc5ed12818295/gert/libgit2-1.4.2-x86_64_linux/include -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/bbs-3.19-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpFfSwlB/R.INSTALLfc5ed12818295/gert/libgit2-1.4.2-x86_64_linux/include -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/bbs-3.19-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpFfSwlB/R.INSTALLfc5ed12818295/gert/libgit2-1.4.2-x86_64_linux/include -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/bbs-3.19-bioc/R/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 -L/tmp/RtmpFfSwlB/R.INSTALLfc5ed12818295/gert/libgit2-1.4.2-x86_64_linux/lib -lstatgit2 -lrt -lpthread -lstatssh2 -lstatssl -lstatcrypto -ldl -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpHWD2ve/RLIBS_ebf91d106758/00LOCK-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 (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c pause.c -o pause.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c profvis-init.c -o profvis-init.o
gcc -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o profvis.so pause.o profvis-init.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpHWD2ve/RLIBS_ebf91d106758/00LOCK-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++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/cpp11/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c cpp11.cpp -o cpp11.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/cpp11/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c escapeExamples.cpp -o escapeExamples.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/cpp11/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c isComplete.cpp -o isComplete.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/cpp11/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c leadingSpaces.cpp -o leadingSpaces.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/cpp11/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c parser2.cpp -o parser2.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/cpp11/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c wrapUsage.cpp -o wrapUsage.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o roxygen2.so cpp11.o escapeExamples.o isComplete.o leadingSpaces.o parser2.o wrapUsage.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpHWD2ve/RLIBS_ebf91d106758/00LOCK-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 libuv found by pkg-config in /usr
** PKG_CFLAGS=
** PKG_LIBS=-luv -lpthread -ldl -lrt
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/later/include' -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/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/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/later/include' -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/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/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/later/include' -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/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/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/later/include' -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/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/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/later/include' -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/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/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/later/include' -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/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/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/later/include' -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/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/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/later/include' -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/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/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/later/include' -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/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/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/later/include' -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/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/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/later/include' -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/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/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/later/include' -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/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/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/later/include' -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/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/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/later/include' -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/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/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/later/include' -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/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/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/later/include' -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/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/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/later/include' -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/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/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/later/include' -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/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/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/later/include' -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/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/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/later/include' -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/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/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/later/include' -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/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/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/later/include' -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/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/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/later/include' -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/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/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/later/include' -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/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/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/later/include' -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/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/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/later/include' -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/Rcpp/include' -I/usr/local/include   -fvisibility=hidden -DSTRICT_R_HEADERS -fpic  -g -O2  -Wall  -c winutils.cpp -o winutils.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/later/include' -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/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/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/later/include' -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/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/bbs-3.19-bioc/R/include" -DNDEBUG -pthread -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/later/include' -I'/tmp/RtmpHWD2ve/RLIBS_ebf91d106758/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/bbs-3.19-bioc/R/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 -luv -lpthread -ldl -lrt ./http-parser/http_parser.o ./sha1/sha1.o ./base64/base64.o -pthread -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpHWD2ve/RLIBS_ebf91d106758/00LOCK-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
	'/tmp/Rtmpb4ObYV/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 (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c bit-ops.c -o bit-ops.o
bit-ops.c: In function ‘bitShiftL’:
bit-ops.c:125:80: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses]
  125 |                 else *(xaAb++)=(double) (_2_UINT_(xa[i]) __OP__ I_2_UINT(xb[j] & 31 ) ) ; \
      |                                                                                ^
bit-ops.c:6:50: note: in definition of macro ‘I_2_UINT’
    6 | #define I_2_UINT(I)   (unsigned int) ((I) < 0 ? (I + UINT_MAX +1) : (I))
      |                                                  ^
bit-ops.c:145:5: note: in expansion of macro ‘bitshift_BODY’
  145 |     bitshift_BODY( << );
      |     ^~~~~~~~~~~~~
bit-ops.c:136:80: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses]
  136 |                 else *(xaAb++)=(double) (_2_UINT_(xa[j]) __OP__ I_2_UINT(xb[i] & 31 )) ; \
      |                                                                                ^
bit-ops.c:6:50: note: in definition of macro ‘I_2_UINT’
    6 | #define I_2_UINT(I)   (unsigned int) ((I) < 0 ? (I + UINT_MAX +1) : (I))
      |                                                  ^
bit-ops.c:145:5: note: in expansion of macro ‘bitshift_BODY’
  145 |     bitshift_BODY( << );
      |     ^~~~~~~~~~~~~
bit-ops.c: In function ‘bitShiftR’:
bit-ops.c:125:80: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses]
  125 |                 else *(xaAb++)=(double) (_2_UINT_(xa[i]) __OP__ I_2_UINT(xb[j] & 31 ) ) ; \
      |                                                                                ^
bit-ops.c:6:50: note: in definition of macro ‘I_2_UINT’
    6 | #define I_2_UINT(I)   (unsigned int) ((I) < 0 ? (I + UINT_MAX +1) : (I))
      |                                                  ^
bit-ops.c:149:5: note: in expansion of macro ‘bitshift_BODY’
  149 |     bitshift_BODY( >> );
      |     ^~~~~~~~~~~~~
bit-ops.c:136:80: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses]
  136 |                 else *(xaAb++)=(double) (_2_UINT_(xa[j]) __OP__ I_2_UINT(xb[i] & 31 )) ; \
      |                                                                                ^
bit-ops.c:6:50: note: in definition of macro ‘I_2_UINT’
    6 | #define I_2_UINT(I)   (unsigned int) ((I) < 0 ? (I + UINT_MAX +1) : (I))
      |                                                  ^
bit-ops.c:149:5: note: in expansion of macro ‘bitshift_BODY’
  149 |     bitshift_BODY( >> );
      |     ^~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c cksum.c -o cksum.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o bitops.so bit-ops.o cksum.o init.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpHWD2ve/RLIBS_ebf91d106758/00LOCK-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 7.81.0
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include    -fpic  -g -O2  -Wall -c base64.c -o base64.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include    -fpic  -g -O2  -Wall -c curl.c -o curl.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include    -fpic  -g -O2  -Wall -c curlInit.c -o curlInit.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include    -fpic  -g -O2  -Wall -c curl_base64.c -o curl_base64.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include    -fpic  -g -O2  -Wall -c enums.c -o enums.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include    -fpic  -g -O2  -Wall -c json.c -o json.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include    -fpic  -g -O2  -Wall -c memoryManagement.c -o memoryManagement.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include    -fpic  -g -O2  -Wall -c myUTF8.c -o myUTF8.o
gcc -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o RCurl.so base64.o curl.o curlInit.o curl_base64.o enums.o json.o memoryManagement.o myUTF8.o -lcurl -lxml2 -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /tmp/RtmpHWD2ve/RLIBS_ebf91d106758/00LOCK-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
	'/tmp/Rtmpb4ObYV/downloaded_packages'
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/tmp/Rtmpb4ObYV/remotesf7244754d9e62/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 
397.702  33.061 434.168
name	user	system	elapsed
plotAbundance	10.156	0.484	10.641
plotAbundanceDensity	11.922	0.960	13.446
plotCCA	5.920	0.304	6.224
plotColTile	0.642	0.007	0.650
plotDMN	19.047	0.088	19.134
plotGraph	0	0	0
plotPrevalence	7.706	0.155	7.862
plotSeries	0	0	0
plotTree	49.677	1.015	50.705
treeData	0.652	0.016	0.668
CHECK results for miaViz on nebbiolo1

Summary

Command output

Installation output

Tests output

Example timings
