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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MatrixQCvis.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings MatrixQCvis_1.7.4.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MatrixQCvis.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘MatrixQCvis/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MatrixQCvis’ version ‘1.7.4’
* 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 ‘MatrixQCvis’ 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Expected match: "trying to get slot"
  Actual message: "no applicable method for `@` applied to an object of class \"NULL\""
  Backtrace:
      ▆
   1. ├─testthat::expect_error(...) at test_tab_measuredvalues_missingvalues.R:161:4
   2. │ └─testthat:::quasi_capture(...)
   3. │   ├─testthat (local) .capture(...)
   4. │   │ └─base::withCallingHandlers(...)
   5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   6. └─MatrixQCvis::extractComb(...)
   7.   └─MatrixQCvis::measuredCategory(se = se, measured = measured, category = category)
  
  [ FAIL 4 | WARN 2 | SKIP 0 | PASS 459 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘MatrixQCvis.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘MatrixQCvis.Rmd’ using rmarkdown
trying URL 'https://cloud.r-project.org/src/contrib/prettyunits_1.1.1.tar.gz'
Content type 'application/x-gzip' length 10366 bytes (10 KB)
==================================================
downloaded 10 KB

trying URL 'https://cloud.r-project.org/src/contrib/progress_1.2.2.tar.gz'
Content type 'application/x-gzip' length 29506 bytes (28 KB)
==================================================
downloaded 28 KB

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)
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downloaded 21 KB

trying URL 'https://cloud.r-project.org/src/contrib/hms_1.1.3.tar.gz'
Content type 'application/x-gzip' length 43379 bytes (42 KB)
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downloaded 42 KB

trying URL 'https://cloud.r-project.org/src/contrib/vroom_1.6.1.tar.gz'
Content type 'application/x-gzip' length 719742 bytes (702 KB)
==================================================
downloaded 702 KB

trying URL 'https://cloud.r-project.org/src/contrib/tzdb_0.3.0.tar.gz'
Content type 'application/x-gzip' length 567544 bytes (554 KB)
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downloaded 554 KB

trying URL 'https://cloud.r-project.org/src/contrib/R.oo_1.25.0.tar.gz'
Content type 'application/x-gzip' length 384384 bytes (375 KB)
==================================================
downloaded 375 KB

trying URL 'https://cloud.r-project.org/src/contrib/R.methodsS3_1.8.2.tar.gz'
Content type 'application/x-gzip' length 24131 bytes (23 KB)
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downloaded 23 KB

trying URL 'https://cloud.r-project.org/src/contrib/readr_2.1.4.tar.gz'
Content type 'application/x-gzip' length 298083 bytes (291 KB)
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downloaded 291 KB

trying URL 'https://cloud.r-project.org/src/contrib/xml2_1.3.3.tar.gz'
Content type 'application/x-gzip' length 283965 bytes (277 KB)
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downloaded 277 KB

trying URL 'https://cloud.r-project.org/src/contrib/R.utils_2.12.2.tar.gz'
Content type 'application/x-gzip' length 365876 bytes (357 KB)
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downloaded 357 KB

trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/GEOquery_2.67.0.tar.gz'
Content type 'application/x-gzip' length 13696127 bytes (13.1 MB)
==================================================
downloaded 13.1 MB

trying URL 'https://bioconductor.org/packages/3.17/data/experiment/src/contrib/GSE62944_1.27.0.tar.gz'
Content type 'application/x-gzip' length 226612 bytes (221 KB)
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downloaded 221 KB

* 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 ‘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 ‘hms’ ...
** package ‘hms’ 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 (hms)
* installing *source* package ‘tzdb’ ...
** package ‘tzdb’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I/usr/local/include   -I../inst/include -DINSTALL=dummy -DAUTO_DOWNLOAD=0 -DHAS_REMOTE_API=0 -DUSE_OS_TZDB=0 -DONLY_C_LOCALE=1 -fpic  -g -O2  -Wall -c api.cpp -o api.o
In file included from api.cpp:3:
/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include/cpp11/protect.hpp:430:1: warning: ‘cpp11::preserved’ defined but not used [-Wunused-variable]
  430 | preserved;
      | ^~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I/usr/local/include   -I../inst/include -DINSTALL=dummy -DAUTO_DOWNLOAD=0 -DHAS_REMOTE_API=0 -DUSE_OS_TZDB=0 -DONLY_C_LOCALE=1 -fpic  -g -O2  -Wall -c cpp11.cpp -o cpp11.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I/usr/local/include   -I../inst/include -DINSTALL=dummy -DAUTO_DOWNLOAD=0 -DHAS_REMOTE_API=0 -DUSE_OS_TZDB=0 -DONLY_C_LOCALE=1 -fpic  -g -O2  -Wall -c names.cpp -o names.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I/usr/local/include   -I../inst/include -DINSTALL=dummy -DAUTO_DOWNLOAD=0 -DHAS_REMOTE_API=0 -DUSE_OS_TZDB=0 -DONLY_C_LOCALE=1 -fpic  -g -O2  -Wall -c path.cpp -o path.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I/usr/local/include   -I../inst/include -DINSTALL=dummy -DAUTO_DOWNLOAD=0 -DHAS_REMOTE_API=0 -DUSE_OS_TZDB=0 -DONLY_C_LOCALE=1 -fpic  -g -O2  -Wall -c tz.cpp -o tz.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I/usr/local/include   -I../inst/include -DINSTALL=dummy -DAUTO_DOWNLOAD=0 -DHAS_REMOTE_API=0 -DUSE_OS_TZDB=0 -DONLY_C_LOCALE=1 -fpic  -g -O2  -Wall -c version.cpp -o version.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o tzdb.so api.o cpp11.o names.o path.o tz.o version.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/00LOCK-tzdb/00new/tzdb/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 (tzdb)
* installing *source* package ‘R.methodsS3’ ...
** package ‘R.methodsS3’ 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 (R.methodsS3)
* 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 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-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-3.17-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-3.17-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-3.17-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-3.17-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-3.17-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-3.17-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-3.17-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-3.17-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-3.17-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-3.17-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-3.17-bioc/R/lib -lR
installing to /tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/00LOCK-xml2/00new/xml2/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 (xml2)
* installing *source* package ‘progress’ ...
** package ‘progress’ 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 (progress)
* installing *source* package ‘R.oo’ ...
** package ‘R.oo’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning in setGenericS3.default(name, export = exportGeneric, envir = envir,  :
  Renamed the preexisting function getMethods to getMethods.default, which was defined in environment R.oo.
Warning in setGenericS3.default(name, export = exportGeneric, envir = envir,  :
  Renamed the preexisting function getClasses to getClasses.default, which was defined in environment R.oo.
** 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 (R.oo)
* installing *source* package ‘vroom’ ...
** package ‘vroom’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/progress/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c Iconv.cpp -o Iconv.o
In file included from Iconv.cpp:2:
/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include/cpp11/protect.hpp:430:1: warning: ‘cpp11::preserved’ defined but not used [-Wunused-variable]
  430 | preserved;
      | ^~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/progress/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c LocaleInfo.cpp -o LocaleInfo.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/progress/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c altrep.cc -o altrep.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/progress/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c cpp11.cpp -o cpp11.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/progress/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c delimited_index.cc -o delimited_index.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/progress/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c delimited_index_connection.cc -o delimited_index_connection.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/progress/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c fixed_width_index_connection.cc -o fixed_width_index_connection.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/progress/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c gen.cc -o gen.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/progress/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c grisu3.c -o grisu3.o
grisu3.c: In function ‘double2diy_fp’:
grisu3.c:57:23: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   57 | #define CAST_U64(d) (*(uint64_t*)&d)
      |                       ^
grisu3.c:209:24: note: in expansion of macro ‘CAST_U64’
  209 |         uint64_t u64 = CAST_U64(d);
      |                        ^~~~~~~~
grisu3.c: In function ‘grisu3’:
grisu3.c:57:23: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   57 | #define CAST_U64(d) (*(uint64_t*)&d)
      |                       ^
grisu3.c:296:24: note: in expansion of macro ‘CAST_U64’
  296 |         uint64_t u64 = CAST_U64(v);
      |                        ^~~~~~~~
grisu3.c: In function ‘dtoa_grisu3’:
grisu3.c:57:23: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   57 | #define CAST_U64(d) (*(uint64_t*)&d)
      |                       ^
grisu3.c:346:24: note: in expansion of macro ‘CAST_U64’
  346 |         uint64_t u64 = CAST_U64(v);
      |                        ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/progress/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c guess_type.cc -o guess_type.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/progress/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c iconv_file.cc -o iconv_file.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/progress/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c index_collection.cc -o index_collection.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/progress/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c vroom.cc -o vroom.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/progress/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c vroom_big_int.cc -o vroom_big_int.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/progress/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c vroom_chr.cc -o vroom_chr.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/progress/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c vroom_date.cc -o vroom_date.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/progress/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c vroom_dbl.cc -o vroom_dbl.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/progress/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c vroom_dttm.cc -o vroom_dttm.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/progress/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c vroom_errors.cpp -o vroom_errors.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/progress/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c vroom_fct.cc -o vroom_fct.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/progress/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c vroom_fwf.cc -o vroom_fwf.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/progress/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c vroom_int.cc -o vroom_int.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/progress/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c vroom_num.cc -o vroom_num.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/progress/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c vroom_rle.cc -o vroom_rle.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/progress/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c vroom_time.cc -o vroom_time.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/progress/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c vroom_write.cc -o vroom_write.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o vroom.so Iconv.o LocaleInfo.o altrep.o cpp11.o delimited_index.o delimited_index_connection.o fixed_width_index_connection.o gen.o grisu3.o guess_type.o iconv_file.o index_collection.o vroom.o vroom_big_int.o vroom_chr.o vroom_date.o vroom_dbl.o vroom_dttm.o vroom_errors.o vroom_fct.o vroom_fwf.o vroom_int.o vroom_num.o vroom_rle.o vroom_time.o vroom_write.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/00LOCK-vroom/00new/vroom/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 (vroom)
* installing *source* package ‘R.utils’ ...
** package ‘R.utils’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning in setGenericS3.default(name, export = exportGeneric, envir = envir,  :
  Renamed the preexisting function warnings to warnings.default, which was defined in environment R.utils.
** 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 (R.utils)
* installing *source* package ‘readr’ ...
** package ‘readr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c Collector.cpp -o Collector.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c CollectorGuess.cpp -o CollectorGuess.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c Iconv.cpp -o Iconv.o
In file included from Iconv.cpp:2:
/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include/cpp11/protect.hpp:430:1: warning: ‘cpp11::preserved’ defined but not used [-Wunused-variable]
  430 | preserved;
      | ^~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c LocaleInfo.cpp -o LocaleInfo.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c Reader.cpp -o Reader.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c Source.cpp -o Source.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c Tokenizer.cpp -o Tokenizer.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c TokenizerDelim.cpp -o TokenizerDelim.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c TokenizerFwf.cpp -o TokenizerFwf.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c TokenizerWs.cpp -o TokenizerWs.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c connection.cpp -o connection.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c cpp11.cpp -o cpp11.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c datetime.cpp -o datetime.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c grisu3.c -o grisu3.o
grisu3.c: In function ‘double2diy_fp’:
grisu3.c:57:23: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   57 | #define CAST_U64(d) (*(uint64_t*)&d)
      |                       ^
grisu3.c:209:24: note: in expansion of macro ‘CAST_U64’
  209 |         uint64_t u64 = CAST_U64(d);
      |                        ^~~~~~~~
grisu3.c: In function ‘grisu3’:
grisu3.c:57:23: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   57 | #define CAST_U64(d) (*(uint64_t*)&d)
      |                       ^
grisu3.c:304:24: note: in expansion of macro ‘CAST_U64’
  304 |         uint64_t u64 = CAST_U64(v);
      |                        ^~~~~~~~
grisu3.c: In function ‘dtoa_grisu3’:
grisu3.c:57:23: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   57 | #define CAST_U64(d) (*(uint64_t*)&d)
      |                       ^
grisu3.c:356:24: note: in expansion of macro ‘CAST_U64’
  356 |         uint64_t u64 = CAST_U64(v);
      |                        ^~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c parse.cpp -o parse.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c read.cpp -o read.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c type_convert.cpp -o type_convert.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c write.cpp -o write.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/cpp11/include' -I'/tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c write_delim.cpp -o write_delim.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o readr.so Collector.o CollectorGuess.o Iconv.o LocaleInfo.o Reader.o Source.o Tokenizer.o TokenizerDelim.o TokenizerFwf.o TokenizerWs.o connection.o cpp11.o datetime.o grisu3.o init.o parse.o read.o type_convert.o write.o write_delim.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpUEV1wV/RLIBS_2d8da73b5757af/00LOCK-readr/00new/readr/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 (readr)
* installing *source* package ‘GEOquery’ ...
** 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 (GEOquery)
* installing *source* package ‘GSE62944’ ...
** using staged installation
** inst
** 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 (GSE62944)

The downloaded source packages are in
	'/tmp/Rtmpi4EaR7/downloaded_packages'
Failed with error:  'there is no package called 'jpeg''
Quitting from lines 523-527 (MatrixQCvis.Rmd) 
Error: processing vignette 'MatrixQCvis.Rmd' failed with diagnostics:
Need jpeg package to read image.
--- failed re-building ‘MatrixQCvis.Rmd’

SUMMARY: processing the following file failed:
  ‘MatrixQCvis.Rmd’

Error: Vignette re-building failed.
Execution halted

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

Status: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/MatrixQCvis.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL MatrixQCvis
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘MatrixQCvis’ ...
** 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 (MatrixQCvis)

R version 4.3.0 alpha (2023-04-03 r84154)
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> library(testthat)
> library(MatrixQCvis)
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 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: plotly
Loading required package: ggplot2

Attaching package: 'plotly'

The following object is masked from 'package:ggplot2':

    last_plot

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

    slice

The following object is masked from 'package:S4Vectors':

    rename

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

    filter

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

    layout

Loading required package: shiny
> testthat::test_check("MatrixQCvis")
initial  value 0.091643 
final  value 0.091636 
converged
initial  value 0.091643 
final  value 0.091636 
converged
[1] 28.64894
[ FAIL 4 | WARN 2 | SKIP 0 | PASS 459 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_tab_dimensionreduction.R:142:5'): dimensionReductionPlot ─────
`dimensionReductionPlot(tbl = tbl, se = "foo")` threw an error with unexpected message.
Expected match: "trying to get slot"
Actual message: "no applicable method for `@` applied to an object of class \"character\""
Backtrace:
     ▆
  1. ├─testthat::expect_error(...) at test_tab_dimensionreduction.R:142:4
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. └─MatrixQCvis::dimensionReductionPlot(tbl = tbl, se = "foo")
  7.   ├─base::match.arg(highlight)
  8.   │ └─base::eval(formal.args[[as.character(substitute(arg))]], envir = sys.frame(sysP))
  9.   │   └─base::eval(formal.args[[as.character(substitute(arg))]], envir = sys.frame(sysP))
 10.   └─base::colnames(se@colData)
 11.     └─base::is.data.frame(x)
── Failure ('test_tab_measuredvalues_missingvalues.R:88:5'): measuredCategory ──
`measuredCategory(se = NULL, measured = TRUE, category = "type")` threw an error with unexpected message.
Expected match: "trying to get slot"
Actual message: "no applicable method for `@` applied to an object of class \"NULL\""
Backtrace:
    ▆
 1. ├─testthat::expect_error(...) at test_tab_measuredvalues_missingvalues.R:88:4
 2. │ └─testthat:::quasi_capture(...)
 3. │   ├─testthat (local) .capture(...)
 4. │   │ └─base::withCallingHandlers(...)
 5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
 6. └─MatrixQCvis::measuredCategory(se = NULL, measured = TRUE, category = "type")
── Failure ('test_tab_measuredvalues_missingvalues.R:100:5'): histFeatureCategory ──
`histFeatureCategory(...)` threw an error with unexpected message.
Expected match: "trying to get slot"
Actual message: "no applicable method for `@` applied to an object of class \"NULL\""
Backtrace:
    ▆
 1. ├─testthat::expect_error(...) at test_tab_measuredvalues_missingvalues.R:100:4
 2. │ └─testthat:::quasi_capture(...)
 3. │   ├─testthat (local) .capture(...)
 4. │   │ └─base::withCallingHandlers(...)
 5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
 6. └─MatrixQCvis::histFeatureCategory(...)
 7.   └─MatrixQCvis::measuredCategory(se, measured = measured, category = category)
── Failure ('test_tab_measuredvalues_missingvalues.R:161:5'): extractComb ──────
`extractComb(se = NULL, combination = "1", measured = TRUE, category = "type")` threw an error with unexpected message.
Expected match: "trying to get slot"
Actual message: "no applicable method for `@` applied to an object of class \"NULL\""
Backtrace:
    ▆
 1. ├─testthat::expect_error(...) at test_tab_measuredvalues_missingvalues.R:161:4
 2. │ └─testthat:::quasi_capture(...)
 3. │   ├─testthat (local) .capture(...)
 4. │   │ └─base::withCallingHandlers(...)
 5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
 6. └─MatrixQCvis::extractComb(...)
 7.   └─MatrixQCvis::measuredCategory(se = se, measured = measured, category = category)

[ FAIL 4 | WARN 2 | SKIP 0 | PASS 459 ]
Error: Test failures
Execution halted