| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:06:44 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the IgGeneUsage package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/IgGeneUsage.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 916/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| IgGeneUsage 1.8.0 (landing page) Simo Kitanovski
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: IgGeneUsage |
| Version: 1.8.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IgGeneUsage.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings IgGeneUsage_1.8.0.tar.gz |
| StartedAt: 2022-04-12 21:21:26 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 21:42:55 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 1289.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: IgGeneUsage.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IgGeneUsage.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings IgGeneUsage_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/IgGeneUsage.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'IgGeneUsage/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'IgGeneUsage' version '1.8.0'
* 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 ... NOTE
Found the following hidden files and directories:
.travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'IgGeneUsage' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
4. | \-withr::with_path(rtools_path(), code)
5. | \-base::force(code)
6. \-inline::cxxfunction(...)
7. \-inline:::compileCode(f, code, language = language, verbose = verbose)
-- Error (test-model.R:8:3): stan model availability check ---------------------
Error in `sink(type = "output")`: invalid connection
Backtrace:
x
1. \-rstan::stan_model(file = model.file, auto_write = TRUE) at test-model.R:8:2
2. \-rstan:::cxxfunctionplus(...)
3. \-base::sink(type = "output")
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 89 ]
Error: Test failures
Execution halted
** running tests for arch 'x64' ...
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
4. | \-withr::with_path(rtools_path(), code)
5. | \-base::force(code)
6. \-inline::cxxfunction(...)
7. \-inline:::compileCode(f, code, language = language, verbose = verbose)
-- Error (test-model.R:8:3): stan model availability check ---------------------
Error in `sink(type = "output")`: invalid connection
Backtrace:
x
1. \-rstan::stan_model(file = model.file, auto_write = TRUE) at test-model.R:8:2
2. \-rstan:::cxxfunctionplus(...)
3. \-base::sink(type = "output")
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 89 ]
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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.14-bioc/meat/IgGeneUsage.Rcheck/00check.log'
for details.
IgGeneUsage.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/IgGeneUsage_1.8.0.tar.gz && rm -rf IgGeneUsage.buildbin-libdir && mkdir IgGeneUsage.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=IgGeneUsage.buildbin-libdir IgGeneUsage_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL IgGeneUsage_1.8.0.zip && rm IgGeneUsage_1.8.0.tar.gz IgGeneUsage_1.8.0.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
46 98k 46 47039 0 0 297k 0 --:--:-- --:--:-- --:--:-- 298k
100 98k 100 98k 0 0 432k 0 --:--:-- --:--:-- --:--:-- 431k
install for i386
* installing *source* package 'IgGeneUsage' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'IgGeneUsage'
finding HTML links ... done
DGU html
IGHV_Epitopes html
IGHV_HCV html
Ig html
Ig_SE html
LOO html
** 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
install for x64
* installing *source* package 'IgGeneUsage' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'IgGeneUsage' as IgGeneUsage_1.8.0.zip
* DONE (IgGeneUsage)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'IgGeneUsage' successfully unpacked and MD5 sums checked
|
IgGeneUsage.Rcheck/tests_i386/testthat.Rout.fail
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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(IgGeneUsage)
Loading required package: Rcpp
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, 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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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: StanHeaders
>
> test_check("IgGeneUsage")
Tests Frequentist methods
Tests Summarized Experiment check
Tests input rules
Tests stan model
make cmd is
make -f "C:/Users/BIOCBU~1/BBS-3~1.14-/R/etc/i386/Makeconf" -f "C:/Users/BIOCBU~1/BBS-3~1.14-/R/share/make/winshlib.mk" CXX='$(CXX14) $(CXX14STD)' CXXFLAGS='$(CXX14FLAGS)' CXXPICFLAGS='$(CXX14PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX14LDFLAGS)' SHLIB_LD='$(SHLIB_CXX14LD)' SHLIB="file1f1874392c9a.dll" OBJECTS="file1f1874392c9a.o"
make would use
if test "zfile1f1874392c9a.o" != "z"; then \
if test -e "file1f1874392c9a-win.def"; then \
echo "C:/rtools40/mingw32/bin/"g++ -shared -s -static-libgcc -o file1f1874392c9a.dll file1f1874392c9a-win.def file1f1874392c9a.o -L"C:/extsoft/lib/i386" -L"C:/extsoft/lib" -L"C:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386" -lR ; \
"C:/rtools40/mingw32/bin/"g++ -shared -s -static-libgcc -o file1f1874392c9a.dll file1f1874392c9a-win.def file1f1874392c9a.o -L"C:/extsoft/lib/i386" -L"C:/extsoft/lib" -L"C:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386" -lR ; \
else \
echo EXPORTS > tmp.def; \
"C:/rtools40/mingw32/bin/"nm file1f1874392c9a.o | sed -n 's/^.* [BCDRT] _/ /p' | sed 's/[^ ][^ ]*/"&"/g' >> tmp.def; \
echo "C:/rtools40/mingw32/bin/"g++ -shared -s -static-libgcc -o file1f1874392c9a.dll tmp.def file1f1874392c9a.o -L"C:/extsoft/lib/i386" -L"C:/extsoft/lib" -L"C:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386" -lR ; \
"C:/rtools40/mingw32/bin/"g++ -shared -s -static-libgcc -o file1f1874392c9a.dll tmp.def file1f1874392c9a.o -L"C:/extsoft/lib/i386" -L"C:/extsoft/lib" -L"C:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386" -lR ; \
rm -f tmp.def; \
fi \
fi
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 89 ]
== Failed tests ================================================================
-- Error (test-model.R:8:3): stan model availability check ---------------------
Error in `compileCode(f, code, language = language, verbose = verbose)`: C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: file1f1874392c9a.o:file1f1874392c9a.cpp:(.text$_ZN3tbb8internal26task_scheduler_observer_v3D0Ev[__ZN3tbb8internal26task_scheduler_observer_v3D0Ev]+0x1b): undefined reference to `tbb::internal::task_scheduler_observer_v3::observe(bool)'C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: file1f1874392c9a.o:file1f1874392c9a.cpp:(.text$_ZN3tbb10interface623task_scheduler_observerD0Ev[__ZN3tbb10interface623task_scheduler_observerD0Ev]+0x1b): undefined reference to `tbb::internal::task_scheduler_observer_v3::observe(bool)'C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: file1f1874392c9a.o:file1f1874392c9a.cpp:(.text$_ZN3tbb10interface623task_scheduler_observerD0Ev[__ZN3tbb10interface623task_scheduler_observerD0Ev]+0x39): undefined reference to `tbb::internal::task_scheduler_observer_v3::observe(bool)'C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: file1f1874392c9a.o:file1f1874392c9a.cpp:(.text$_ZN3tbb10interface623task_scheduler_observerD1Ev[__ZN3tbb10interface623task_scheduler_observerD1Ev]+0x1b): undefined reference to `tbb::internal::task_scheduler_observer_v3::observe(bool)'C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: file1f1874392c9a.o:file1f1874392c9a.cpp:(.text$_ZN3tbb10interface623task_scheduler_observerD1Ev[__ZN3tbb10interface623task_scheduler_observerD1Ev]+0x39): more undefined references to `tbb::internal::task_scheduler_observer_v3::observe(bool)' followcollect2.exe: error: ld returned 1 exit status
Backtrace:
x
1. \-rstan::stan_model(file = model.file, auto_write = TRUE) at test-model.R:8:2
2. \-rstan:::cxxfunctionplus(...)
3. +-pkgbuild::with_build_tools(...)
4. | \-withr::with_path(rtools_path(), code)
5. | \-base::force(code)
6. \-inline::cxxfunction(...)
7. \-inline:::compileCode(f, code, language = language, verbose = verbose)
-- Error (test-model.R:8:3): stan model availability check ---------------------
Error in `sink(type = "output")`: invalid connection
Backtrace:
x
1. \-rstan::stan_model(file = model.file, auto_write = TRUE) at test-model.R:8:2
2. \-rstan:::cxxfunctionplus(...)
3. \-base::sink(type = "output")
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 89 ]
Error: Test failures
Execution halted
|
IgGeneUsage.Rcheck/tests_x64/testthat.Rout.fail
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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(IgGeneUsage)
Loading required package: Rcpp
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, 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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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: StanHeaders
>
> test_check("IgGeneUsage")
Tests Frequentist methods
Tests Summarized Experiment check
Tests input rules
Tests stan model
make cmd is
make -f "C:/Users/BIOCBU~1/BBS-3~1.14-/R/etc/x64/Makeconf" -f "C:/Users/BIOCBU~1/BBS-3~1.14-/R/share/make/winshlib.mk" CXX='$(CXX14) $(CXX14STD)' CXXFLAGS='$(CXX14FLAGS)' CXXPICFLAGS='$(CXX14PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX14LDFLAGS)' SHLIB_LD='$(SHLIB_CXX14LD)' SHLIB="file1c3428402af0.dll" WIN=64 TCLBIN=64 OBJECTS="file1c3428402af0.o"
make would use
if test "zfile1c3428402af0.o" != "z"; then \
if test -e "file1c3428402af0-win.def"; then \
echo "C:/rtools40/mingw64/bin/"g++ -shared -s -static-libgcc -o file1c3428402af0.dll file1c3428402af0-win.def file1c3428402af0.o -L"C:/extsoft/lib/x64" -L"C:/extsoft/lib" -L"C:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64" -lR ; \
"C:/rtools40/mingw64/bin/"g++ -shared -s -static-libgcc -o file1c3428402af0.dll file1c3428402af0-win.def file1c3428402af0.o -L"C:/extsoft/lib/x64" -L"C:/extsoft/lib" -L"C:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64" -lR ; \
else \
echo EXPORTS > tmp.def; \
"C:/rtools40/mingw64/bin/"nm file1c3428402af0.o | sed -n 's/^.* [BCDRT] / /p' | sed -e '/[.]refptr[.]/d' -e '/[.]weak[.]/d' | sed 's/[^ ][^ ]*/"&"/g' >> tmp.def; \
echo "C:/rtools40/mingw64/bin/"g++ -shared -s -static-libgcc -o file1c3428402af0.dll tmp.def file1c3428402af0.o -L"C:/extsoft/lib/x64" -L"C:/extsoft/lib" -L"C:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64" -lR ; \
"C:/rtools40/mingw64/bin/"g++ -shared -s -static-libgcc -o file1c3428402af0.dll tmp.def file1c3428402af0.o -L"C:/extsoft/lib/x64" -L"C:/extsoft/lib" -L"C:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64" -lR ; \
rm -f tmp.def; \
fi \
fi
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 89 ]
== Failed tests ================================================================
-- Error (test-model.R:8:3): stan model availability check ---------------------
Error in `compileCode(f, code, language = language, verbose = verbose)`: C:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: file1c3428402af0.o:file1c3428402af0.cpp:(.text$_ZN3tbb10interface623task_scheduler_observerD1Ev[_ZN3tbb10interface623task_scheduler_observerD1Ev]+0x1c): more undefined references to `tbb::internal::task_scheduler_observer_v3::observe(bool)' followcollect2.exe: error: ld returned 1 exit statusC:\rtools40\mingw32\bin\nm.exe: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpsPrUIg/file1c3428402af0.o: file format not recognizedWarning message:In system(sprintf("%s -Pg %s", nm, shQuote(f)), intern = TRUE) : running command 'C:\rtools40\mingw32\bin\nm.exe -Pg "C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpsPrUIg/file1c3428402af0.o"' had status 1
Backtrace:
x
1. \-rstan::stan_model(file = model.file, auto_write = TRUE) at test-model.R:8:2
2. \-rstan:::cxxfunctionplus(...)
3. +-pkgbuild::with_build_tools(...)
4. | \-withr::with_path(rtools_path(), code)
5. | \-base::force(code)
6. \-inline::cxxfunction(...)
7. \-inline:::compileCode(f, code, language = language, verbose = verbose)
-- Error (test-model.R:8:3): stan model availability check ---------------------
Error in `sink(type = "output")`: invalid connection
Backtrace:
x
1. \-rstan::stan_model(file = model.file, auto_write = TRUE) at test-model.R:8:2
2. \-rstan:::cxxfunctionplus(...)
3. \-base::sink(type = "output")
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 89 ]
Error: Test failures
Execution halted
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IgGeneUsage.Rcheck/examples_i386/IgGeneUsage-Ex.timings
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IgGeneUsage.Rcheck/examples_x64/IgGeneUsage-Ex.timings
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