This page was generated on 2020-10-17 11:56:51 -0400 (Sat, 17 Oct 2020).
IgGeneUsage 1.2.2 Simo Kitanovski
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
URL: https://git.bioconductor.org/packages/IgGeneUsage |
Branch: RELEASE_3_11 |
Last Commit: 6e5bdb3 |
Last Changed Date: 2020-07-31 19:10:01 -0400 (Fri, 31 Jul 2020) |
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | |
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | [ ERROR ] | skipped | skipped | |
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### chmod a+r IgGeneUsage -R && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data IgGeneUsage
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* checking for file 'IgGeneUsage/DESCRIPTION' ... OK
* preparing 'IgGeneUsage':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'IgUsageCaseStudies.Rmd' using rmarkdown
Loading required package: IgGeneUsage
Loading required package: Rcpp
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
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")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
Loading required package: StanHeaders
Loading required package: knitr
Loading required package: ggplot2
Loading required package: ggforce
Loading required package: gridExtra
Attaching package: 'gridExtra'
The following object is masked from 'package:Biobase':
combine
The following object is masked from 'package:BiocGenerics':
combine
Loading required package: ggrepel
Loading required package: rstan
rstan (Version 2.21.2, GitRev: 2e1f913d3ca3)
For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores()).
To avoid recompilation of unchanged Stan programs, we recommend calling
rstan_options(auto_write = TRUE)
Do not specify '-march=native' in 'LOCAL_CPPFLAGS' or a Makevars file
Loading required package: reshape2
Compiling model ...
make cmd is
make -f "C:/Users/BIOCBU~1/BBS-3~1.11-/R/etc/x64/Makeconf" -f "C:/Users/BIOCBU~1/BBS-3~1.11-/R/share/make/winshlib.mk" CXX='$(CXX14) $(CXX14STD)' CXXFLAGS='$(CXX14FLAGS)' CXXPICFLAGS='$(CXX14PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX14LDFLAGS)' SHLIB_LD='$(SHLIB_CXX14LD)' SHLIB="filefd82ac31ed.dll" WIN=64 TCLBIN=64 OBJECTS="filefd82ac31ed.o"
make would use
if test "zfilefd82ac31ed.o" != "z"; then \
if test -e "filefd82ac31ed-win.def"; then \
echo "C:/rtools40/mingw64/bin/"g++ -shared -s -static-libgcc -o filefd82ac31ed.dll filefd82ac31ed-win.def filefd82ac31ed.o -L"C:/extsoft/lib/x64" -L"C:/extsoft/lib" -L"C:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64" -lR ; \
"C:/rtools40/mingw64/bin/"g++ -shared -s -static-libgcc -o filefd82ac31ed.dll filefd82ac31ed-win.def filefd82ac31ed.o -L"C:/extsoft/lib/x64" -L"C:/extsoft/lib" -L"C:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64" -lR ; \
else \
echo EXPORTS > tmp.def; \
"C:/rtools40/mingw64/bin/"nm filefd82ac31ed.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 filefd82ac31ed.dll tmp.def filefd82ac31ed.o -L"C:/extsoft/lib/x64" -L"C:/extsoft/lib" -L"C:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64" -lR ; \
"C:/rtools40/mingw64/bin/"g++ -shared -s -static-libgcc -o filefd82ac31ed.dll tmp.def filefd82ac31ed.o -L"C:/extsoft/lib/x64" -L"C:/extsoft/lib" -L"C:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64" -lR ; \
rm -f tmp.def; \
fi \
fi
Quitting from lines 223-231 (IgUsageCaseStudies.Rmd)
Quitting from lines 223-231 (IgUsageCaseStudies.Rmd)
Error: processing vignette 'IgUsageCaseStudies.Rmd' failed with diagnostics:
invalid connection
--- failed re-building 'IgUsageCaseStudies.Rmd'
SUMMARY: processing the following file failed:
'IgUsageCaseStudies.Rmd'
Error: Vignette re-building failed.
Execution halted