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This page was generated on 2022-03-18 11:07:37 -0400 (Fri, 18 Mar 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" 4334
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4097
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" 4083
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" 4134
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

BUILD results for genphen on riesling1


To the developers/maintainers of the genphen package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/genphen.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 763/2090HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genphen 1.23.1  (landing page)
Simo Kitanovski
Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022)
git_url: https://git.bioconductor.org/packages/genphen
git_branch: master
git_last_commit: a3f2476
git_last_commit_date: 2021-11-15 13:28:54 -0400 (Mon, 15 Nov 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    ERROR  skippedskipped
palomino3Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: genphen
Version: 1.23.1
Command: chmod a+r genphen -R && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data genphen
StartedAt: 2022-03-17 16:59:24 -0400 (Thu, 17 Mar 2022)
EndedAt: 2022-03-17 17:00:18 -0400 (Thu, 17 Mar 2022)
EllapsedTime: 54.1 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r genphen -R && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data genphen
###
##############################################################################
##############################################################################


* checking for file 'genphen/DESCRIPTION' ... OK
* preparing 'genphen':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'genphenManual.Rnw' using Sweave
Loading required package: genphen
Loading required package: Rcpp
Warning: Package 'genphen' is deprecated and will be removed from Bioconductor
  version 3.16
Loading required package: ggplot2
Loading required package: knitr
Loading required package: ggrepel
Loading required package: reshape
Loading required package: ape
Loading required package: xtable
Loading required package: gridExtra
Warning: Groups with fewer than two data points have been dropped.
Warning: Groups with fewer than two data points have been dropped.
Warning: Groups with fewer than two data points have been dropped.
Warning: Groups with fewer than two data points have been dropped.
Warning: Groups with fewer than two data points have been dropped.
Warning: Groups with fewer than two data points have been dropped.
Warning: Groups with fewer than two data points have been dropped.
Warning: Groups with fewer than two data points have been dropped.
make cmd is
  make -f "D:/biocbuild/bbs-3.15-bioc/R/etc/x64/Makeconf" -f "D:/biocbuild/bbs-3.15-bioc/R/share/make/winshlib.mk" CXX='$(CXX14) $(CXX14STD)' CXXFLAGS='$(CXX14FLAGS)' CXXPICFLAGS='$(CXX14PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX14LDFLAGS)' SHLIB_LD='$(SHLIB_CXX14LD)' SHLIB="file30c43c574e1e.dll" WIN=64 TCLBIN=64 OBJECTS="file30c43c574e1e.o"

make would use
if test "zfile30c43c574e1e.o" != "z"; then \
  if test -e "file30c43c574e1e-win.def"; then \
    echo "C:/rtools40/mingw64/bin/"g++  -shared -s -static-libgcc -o file30c43c574e1e.dll file30c43c574e1e-win.def file30c43c574e1e.o  -L"C:/extsoft/lib/x64" -L"C:/extsoft/lib"  -L"D:/biocbuild/bbs-3.15-bioc/R/bin/x64" -lR ; \
    "C:/rtools40/mingw64/bin/"g++  -shared -s -static-libgcc -o file30c43c574e1e.dll file30c43c574e1e-win.def file30c43c574e1e.o  -L"C:/extsoft/lib/x64" -L"C:/extsoft/lib"  -L"D:/biocbuild/bbs-3.15-bioc/R/bin/x64" -lR ; \
  else \
    echo EXPORTS > tmp.def; \
    "C:/rtools40/mingw64/bin/"nm file30c43c574e1e.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 file30c43c574e1e.dll tmp.def file30c43c574e1e.o  -L"C:/extsoft/lib/x64" -L"C:/extsoft/lib"  -L"D:/biocbuild/bbs-3.15-bioc/R/bin/x64" -lR ; \
    "C:/rtools40/mingw64/bin/"g++  -shared -s -static-libgcc -o file30c43c574e1e.dll tmp.def file30c43c574e1e.o  -L"C:/extsoft/lib/x64" -L"C:/extsoft/lib"  -L"D:/biocbuild/bbs-3.15-bioc/R/bin/x64" -lR ; \
    rm -f tmp.def; \
  fi \
fi

Error: processing vignette 'genphenManual.Rnw' failed with diagnostics:
 chunk 6 
Error in sink(type = "output") : invalid connection

--- failed re-building 'genphenManual.Rnw'

SUMMARY: processing the following file failed:
  'genphenManual.Rnw'

Error: Vignette re-building failed.
Execution halted