Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-21 13:07:00 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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

CHECK results for RProtoBufLib on tokay2


To the developers/maintainers of the RProtoBufLib package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RProtoBufLib.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 1650/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RProtoBufLib 2.6.0  (landing page)
Mike Jiang
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/RProtoBufLib
git_branch: RELEASE_3_14
git_last_commit: 394836f
git_last_commit_date: 2021-10-26 12:36:04 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: RProtoBufLib
Version: 2.6.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RProtoBufLib.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings RProtoBufLib_2.6.0.tar.gz
StartedAt: 2022-01-21 01:57:14 -0500 (Fri, 21 Jan 2022)
EndedAt: 2022-01-21 01:58:03 -0500 (Fri, 21 Jan 2022)
EllapsedTime: 48.4 seconds
RetCode: 0
Status:   OK  
CheckDir: RProtoBufLib.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RProtoBufLib.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings RProtoBufLib_2.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RProtoBufLib/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RProtoBufLib' version '2.6.0'
* 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 ... NOTE
Found the following non-portable file paths:
  RProtoBufLib/windows/protobuf-3.13.0/include/google/protobuf/compiler/objectivec/objectivec_generator.h
  RProtoBufLib/windows/protobuf-3.13.0/include/google/protobuf/compiler/objectivec/objectivec_helpers.h

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section 'Package structure' in the 'Writing R Extensions' manual.
* checking whether package 'RProtoBufLib' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 168.4Mb
  sub-directories of 1Mb or more:
    include    3.1Mb
    lib      165.2Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components which are templates and need '+ file LICENSE':
  BSD_3_clause
* 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 line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/libs/i386/RProtoBufLib.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RProtoBufLib/libs/x64/RProtoBufLib.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... NONE
* 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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib.Rcheck/00check.log'
for details.



Installation output

RProtoBufLib.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/RProtoBufLib_2.6.0.tar.gz && rm -rf RProtoBufLib.buildbin-libdir && mkdir RProtoBufLib.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RProtoBufLib.buildbin-libdir RProtoBufLib_2.6.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL RProtoBufLib_2.6.0.zip && rm RProtoBufLib_2.6.0.tar.gz RProtoBufLib_2.6.0.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
  0 4622k    0 14635    0     0  27357      0  0:02:53 --:--:--  0:02:53 27355
100 4622k  100 4622k    0     0  3205k      0  0:00:01  0:00:01 --:--:-- 3208k

install for i386

* installing *source* package 'RProtoBufLib' ...
** using staged installation

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
"C:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386/Rscript.exe" "../tools/downloadlibs.R" 3.13.0
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I../inst/include/ -I../windows/protobuf-3.13.0/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c GatingSet_pb_lib/GatingSet.pb.cc -o GatingSet_pb_lib/GatingSet.pb.o
mkdir -p "C:/Users/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib.buildbin-libdir/00LOCK-RProtoBufLib/00new/RProtoBufLib/include"
cp -r ../windows/protobuf-3.13.0/include/google "C:/Users/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib.buildbin-libdir/00LOCK-RProtoBufLib/00new/RProtoBufLib/include"
mkdir -p "C:/Users/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib.buildbin-libdir/00LOCK-RProtoBufLib/00new/RProtoBufLib/lib/i386"
cp  ../windows/protobuf-3.13.0/lib/i386/libprotobuf.a "C:/Users/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib.buildbin-libdir/00LOCK-RProtoBufLib/00new/RProtoBufLib/lib/i386/libprotobuf.a"
cp GatingSet_pb_lib/GatingSet.pb.o "C:/Users/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib.buildbin-libdir/00LOCK-RProtoBufLib/00new/RProtoBufLib/lib/i386/GatingSet.pb.o"
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I../inst/include/ -I../windows/protobuf-3.13.0/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c dummy.cpp -o dummy.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o RProtoBufLib.dll tmp.def dummy.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib.buildbin-libdir/00LOCK-RProtoBufLib/00new/RProtoBufLib/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RProtoBufLib'
    finding HTML links ... done
    LdFlags                                 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 'RProtoBufLib' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
"C:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64/Rscript.exe" "../tools/downloadlibs.R" 3.13.0
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I../inst/include/ -I../windows/protobuf-3.13.0/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c GatingSet_pb_lib/GatingSet.pb.cc -o GatingSet_pb_lib/GatingSet.pb.o
mkdir -p "C:/Users/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib.buildbin-libdir/RProtoBufLib/include"
cp -r ../windows/protobuf-3.13.0/include/google "C:/Users/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib.buildbin-libdir/RProtoBufLib/include"
mkdir -p "C:/Users/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib.buildbin-libdir/RProtoBufLib/lib/x64"
cp  ../windows/protobuf-3.13.0/lib/x64/libprotobuf.a "C:/Users/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib.buildbin-libdir/RProtoBufLib/lib/x64/libprotobuf.a"
cp GatingSet_pb_lib/GatingSet.pb.o "C:/Users/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib.buildbin-libdir/RProtoBufLib/lib/x64/GatingSet.pb.o"
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I../inst/include/ -I../windows/protobuf-3.13.0/include    -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c dummy.cpp -o dummy.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o RProtoBufLib.dll tmp.def dummy.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib.buildbin-libdir/RProtoBufLib/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RProtoBufLib' as RProtoBufLib_2.6.0.zip
* DONE (RProtoBufLib)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'RProtoBufLib' successfully unpacked and MD5 sums checked

Tests output


Example timings