##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:miaViz.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings miaViz_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/miaViz.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘miaViz/DESCRIPTION’ ... OK
* this is package ‘miaViz’ version ‘1.10.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘miaViz’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.rda_plotter: no visible binding for global variable ‘color’
Undefined global functions or variables:
  color
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
plotTree             49.210  1.068  50.374
plotDMN              19.491  0.016  19.508
plotAbundanceDensity 10.467  0.761  11.765
plotPrevalence        8.515  0.220   8.735
plotAbundance         7.019  0.276   7.295
plotCCA               6.314  0.356   6.670
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘miaViz.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/miaViz.Rcheck/00check.log’
for details.

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


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘miaViz’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (miaViz)

R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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

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

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

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

Attaching package: 'MatrixGenerics'

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

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

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, 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'
Content type 'application/x-gzip' length 283844 bytes (277 KB)
==================================================
downloaded 277 KB

trying URL 'https://cloud.r-project.org/src/contrib/zip_2.3.1.tar.gz'
Content type 'application/x-gzip' length 111280 bytes (108 KB)
==================================================
downloaded 108 KB

trying URL 'https://cloud.r-project.org/src/contrib/gitcreds_0.1.2.tar.gz'
Content type 'application/x-gzip' length 62569 bytes (61 KB)
==================================================
downloaded 61 KB

trying URL 'https://cloud.r-project.org/src/contrib/httr2_1.0.0.tar.gz'
Content type 'application/x-gzip' length 212032 bytes (207 KB)
==================================================
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
==================================================
downloaded 3488 bytes

trying URL 'https://cloud.r-project.org/src/contrib/clipr_0.8.0.tar.gz'
Content type 'application/x-gzip' length 21898 bytes (21 KB)
==================================================
downloaded 21 KB

trying URL 'https://cloud.r-project.org/src/contrib/gert_2.0.1.tar.gz'
Content type 'application/x-gzip' length 122723 bytes (119 KB)
==================================================
downloaded 119 KB

trying URL 'https://cloud.r-project.org/src/contrib/gh_1.4.0.tar.gz'
Content type 'application/x-gzip' length 41214 bytes (40 KB)
==================================================
downloaded 40 KB

trying URL 'https://cloud.r-project.org/src/contrib/rstudioapi_0.16.0.tar.gz'
Content type 'application/x-gzip' length 117418 bytes (114 KB)
==================================================
downloaded 114 KB

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)
==================================================
downloaded 27 KB

trying URL 'https://cloud.r-project.org/src/contrib/downlit_0.4.3.tar.gz'
Content type 'application/x-gzip' length 36888 bytes (36 KB)
==================================================
downloaded 36 KB

trying URL 'https://cloud.r-project.org/src/contrib/xml2_1.3.6.tar.gz'
Content type 'application/x-gzip' length 294715 bytes (287 KB)
==================================================
downloaded 287 KB

trying URL 'https://cloud.r-project.org/src/contrib/prettyunits_1.2.0.tar.gz'
Content type 'application/x-gzip' length 97496 bytes (95 KB)
==================================================
downloaded 95 KB

trying URL 'https://cloud.r-project.org/src/contrib/xopen_1.0.0.tar.gz'
Content type 'application/x-gzip' length 11221 bytes (10 KB)
==================================================
downloaded 10 KB

trying URL 'https://cloud.r-project.org/src/contrib/brew_1.0-10.tar.gz'
Content type 'application/x-gzip' length 71087 bytes (69 KB)
==================================================
downloaded 69 KB

trying URL 'https://cloud.r-project.org/src/contrib/usethis_2.2.3.tar.gz'
Content type 'application/x-gzip' length 371088 bytes (362 KB)
==================================================
downloaded 362 KB

trying URL 'https://cloud.r-project.org/src/contrib/ellipsis_0.3.2.tar.gz'
Content type 'application/x-gzip' length 8066 bytes
==================================================
downloaded 8066 bytes

trying URL 'https://cloud.r-project.org/src/contrib/miniUI_0.1.1.1.tar.gz'
Content type 'application/x-gzip' length 97958 bytes (95 KB)
==================================================
downloaded 95 KB

trying URL 'https://cloud.r-project.org/src/contrib/pkgdown_2.0.7.tar.gz'
Content type 'application/x-gzip' length 871465 bytes (851 KB)
==================================================
downloaded 851 KB

trying URL 'https://cloud.r-project.org/src/contrib/profvis_0.3.8.tar.gz'
Content type 'application/x-gzip' length 149012 bytes (145 KB)
==================================================
downloaded 145 KB

trying URL 'https://cloud.r-project.org/src/contrib/rcmdcheck_1.4.0.tar.gz'
Content type 'application/x-gzip' length 73522 bytes (71 KB)
==================================================
downloaded 71 KB

trying URL 'https://cloud.r-project.org/src/contrib/remotes_2.5.0.tar.gz'
Content type 'application/x-gzip' length 164496 bytes (160 KB)
==================================================
downloaded 160 KB

trying URL 'https://cloud.r-project.org/src/contrib/roxygen2_7.3.1.tar.gz'
Content type 'application/x-gzip' length 295558 bytes (288 KB)
==================================================
downloaded 288 KB

trying URL 'https://cloud.r-project.org/src/contrib/rversions_2.1.2.tar.gz'
Content type 'application/x-gzip' length 42135 bytes (41 KB)
==================================================
downloaded 41 KB

trying URL 'https://cloud.r-project.org/src/contrib/sessioninfo_1.2.2.tar.gz'
Content type 'application/x-gzip' length 170924 bytes (166 KB)
==================================================
downloaded 166 KB

trying URL 'https://cloud.r-project.org/src/contrib/urlchecker_1.0.1.tar.gz'
Content type 'application/x-gzip' length 13340 bytes (13 KB)
==================================================
downloaded 13 KB

trying URL 'https://cloud.r-project.org/src/contrib/devtools_2.4.5.tar.gz'
Content type 'application/x-gzip' length 374718 bytes (365 KB)
==================================================
downloaded 365 KB

* 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-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c miniz.c -o miniz.o
gcc -I"/home/biocbuild/bbs-3.18-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-3.18-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-3.18-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-3.18-bioc/R/lib -L/usr/local/lib -o zip.so init.o miniz.o rzip.o zip.o unixutils.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing via 'install.libs.R' to /tmp/RtmpZMwDt2/RLIBS_3736e935172a8/00LOCK-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 ‘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-3.18-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-3.18-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-3.18-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-3.18-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-3.18-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-3.18-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-3.18-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-3.18-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-3.18-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-3.18-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-3.18-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-3.18-bioc/R/lib -lR
installing to /tmp/RtmpZMwDt2/RLIBS_3736e935172a8/00LOCK-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 ‘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 ‘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-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c dots.c -o dots.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o ellipsis.so dots.o init.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /tmp/RtmpZMwDt2/RLIBS_3736e935172a8/00LOCK-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 ‘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 ‘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-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c pause.c -o pause.o
gcc -I"/home/biocbuild/bbs-3.18-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-3.18-bioc/R/lib -L/usr/local/lib -o profvis.so pause.o profvis-init.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /tmp/RtmpZMwDt2/RLIBS_3736e935172a8/00LOCK-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 ‘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 ‘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/Rtmpo41M13/R.INSTALL37c0fb34927826/gert/libgit2-1.4.2-x86_64_linux/include
Using PKG_LIBS=-L/tmp/Rtmpo41M13/R.INSTALL37c0fb34927826/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-3.18-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/Rtmpo41M13/R.INSTALL37c0fb34927826/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-3.18-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/Rtmpo41M13/R.INSTALL37c0fb34927826/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-3.18-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/Rtmpo41M13/R.INSTALL37c0fb34927826/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-3.18-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/Rtmpo41M13/R.INSTALL37c0fb34927826/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-3.18-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/Rtmpo41M13/R.INSTALL37c0fb34927826/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-3.18-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/Rtmpo41M13/R.INSTALL37c0fb34927826/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-3.18-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/Rtmpo41M13/R.INSTALL37c0fb34927826/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-3.18-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/Rtmpo41M13/R.INSTALL37c0fb34927826/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-3.18-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/Rtmpo41M13/R.INSTALL37c0fb34927826/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-3.18-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/Rtmpo41M13/R.INSTALL37c0fb34927826/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-3.18-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/Rtmpo41M13/R.INSTALL37c0fb34927826/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-3.18-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/Rtmpo41M13/R.INSTALL37c0fb34927826/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-3.18-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/Rtmpo41M13/R.INSTALL37c0fb34927826/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-3.18-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/Rtmpo41M13/R.INSTALL37c0fb34927826/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-3.18-bioc/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/Rtmpo41M13/R.INSTALL37c0fb34927826/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-3.18-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/Rtmpo41M13/R.INSTALL37c0fb34927826/gert/libgit2-1.4.2-x86_64_linux/lib -lstatgit2 -lrt -lpthread -lstatssh2 -lstatssl -lstatcrypto -ldl -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /tmp/RtmpZMwDt2/RLIBS_3736e935172a8/00LOCK-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 ‘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-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpZMwDt2/RLIBS_3736e935172a8/cpp11/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c cpp11.cpp -o cpp11.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpZMwDt2/RLIBS_3736e935172a8/cpp11/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c escapeExamples.cpp -o escapeExamples.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpZMwDt2/RLIBS_3736e935172a8/cpp11/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c isComplete.cpp -o isComplete.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpZMwDt2/RLIBS_3736e935172a8/cpp11/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c leadingSpaces.cpp -o leadingSpaces.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpZMwDt2/RLIBS_3736e935172a8/cpp11/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c parser2.cpp -o parser2.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpZMwDt2/RLIBS_3736e935172a8/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-3.18-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-3.18-bioc/R/lib -lR
installing to /tmp/RtmpZMwDt2/RLIBS_3736e935172a8/00LOCK-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 ‘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 ‘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/RtmpzcvH2Y/downloaded_packages'
here         (NA -> 1.0.1 ) [CRAN]
RcppTOML     (NA -> 0.2.2 ) [CRAN]
basilisk.... (NA -> 1.12.1) [CRAN]
dir.expiry   (NA -> 1.8.0 ) [CRAN]
reticulate   (NA -> 1.35.0) [CRAN]
assertthat   (NA -> 0.2.1 ) [CRAN]
basilisk     (NA -> 1.12.1) [CRAN]
densvis      (NA -> 1.10.3) [CRAN]
trying URL 'https://cloud.r-project.org/src/contrib/here_1.0.1.tar.gz'
Content type 'application/x-gzip' length 32954 bytes (32 KB)
==================================================
downloaded 32 KB

trying URL 'https://cloud.r-project.org/src/contrib/RcppTOML_0.2.2.tar.gz'
Content type 'application/x-gzip' length 141195 bytes (137 KB)
==================================================
downloaded 137 KB

trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/basilisk.utils_1.12.1.tar.gz'
Content type 'application/gzip' length 240028 bytes (234 KB)
==================================================
downloaded 234 KB

trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/dir.expiry_1.8.0.tar.gz'
Content type 'application/gzip' length 292895 bytes (286 KB)
==================================================
downloaded 286 KB

trying URL 'https://cloud.r-project.org/src/contrib/reticulate_1.35.0.tar.gz'
Content type 'application/x-gzip' length 1624633 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

trying URL 'https://cloud.r-project.org/src/contrib/assertthat_0.2.1.tar.gz'
Content type 'application/x-gzip' length 12742 bytes (12 KB)
==================================================
downloaded 12 KB

trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/basilisk_1.12.1.tar.gz'
Content type 'application/gzip' length 267290 bytes (261 KB)
==================================================
downloaded 261 KB

trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/densvis_1.10.3.tar.gz'
Content type 'application/gzip' length 1731202 bytes (1.7 MB)
==================================================
downloaded 1.7 MB

* installing *source* package ‘here’ ...
** package ‘here’ 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 (here)
* installing *source* package ‘RcppTOML’ ...
** package ‘RcppTOML’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++17
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I../inst/include -DTOML_ENABLE_FLOAT16=0 -I'/tmp/RtmpZMwDt2/RLIBS_3736e935172a8/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I../inst/include -DTOML_ENABLE_FLOAT16=0 -I'/tmp/RtmpZMwDt2/RLIBS_3736e935172a8/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c parse.cpp -o parse.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o RcppTOML.so RcppExports.o parse.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /tmp/RtmpZMwDt2/RLIBS_3736e935172a8/00LOCK-RcppTOML/00new/RcppTOML/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 (RcppTOML)
* installing *source* package ‘dir.expiry’ ...
** 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 (dir.expiry)
* installing *source* package ‘assertthat’ ...
** package ‘assertthat’ 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 (assertthat)
* installing *source* package ‘basilisk.utils’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (basilisk.utils)
* installing *source* package ‘reticulate’ ...
** package ‘reticulate’ 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-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpZMwDt2/RLIBS_3736e935172a8/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpZMwDt2/RLIBS_3736e935172a8/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c event_loop.cpp -o event_loop.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpZMwDt2/RLIBS_3736e935172a8/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c libpython.cpp -o libpython.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpZMwDt2/RLIBS_3736e935172a8/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c output.cpp -o output.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpZMwDt2/RLIBS_3736e935172a8/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c python.cpp -o python.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpZMwDt2/RLIBS_3736e935172a8/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c readline.cpp -o readline.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpZMwDt2/RLIBS_3736e935172a8/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c signals.cpp -o signals.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o reticulate.so RcppExports.o event_loop.o libpython.o output.o python.o readline.o signals.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /tmp/RtmpZMwDt2/RLIBS_3736e935172a8/00LOCK-reticulate/00new/reticulate/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 (reticulate)
* installing *source* package ‘basilisk’ ...
** using non-staged installation via StagedInstall field
** 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
* DONE (basilisk)
* installing *source* package ‘densvis’ ...
** using non-staged installation via StagedInstall field
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++14
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpZMwDt2/RLIBS_3736e935172a8/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpZMwDt2/RLIBS_3736e935172a8/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c densne.cpp -o densne.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpZMwDt2/RLIBS_3736e935172a8/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c densvis.cpp -o densvis.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpZMwDt2/RLIBS_3736e935172a8/Rcpp/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c sptree.cpp -o sptree.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o densvis.so RcppExports.o densne.o densvis.o sptree.o -llapack -L/home/biocbuild/bbs-3.18-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -fopenmp -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /tmp/RtmpZMwDt2/RLIBS_3736e935172a8/densvis/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
* DONE (densvis)

The downloaded source packages are in
	'/tmp/RtmpzcvH2Y/downloaded_packages'
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/tmp/RtmpzcvH2Y/remotes379c7065e05424/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 12 | SKIP 0 | PASS 215 ]

[ FAIL 0 | WARN 12 | SKIP 0 | PASS 215 ]
> 
> proc.time()
   user  system elapsed 
288.189  21.530 315.246