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CHECK report for cytolib on veracruz1

This page was generated on 2018-04-12 13:45:30 -0400 (Thu, 12 Apr 2018).

Package 324/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cytolib 1.0.1
Mike Jiang
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/cytolib
Branch: RELEASE_3_6
Last Commit: cc476f0
Last Changed Date: 2017-11-03 18:44:20 -0400 (Fri, 03 Nov 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: cytolib
Version: 1.0.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cytolib_1.0.1.tar.gz
StartedAt: 2018-04-12 02:27:35 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 02:29:15 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 100.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: cytolib.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cytolib_1.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/cytolib.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cytolib/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cytolib’ version ‘1.0.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... WARNING
Subdirectory ‘src’ contains:
  GatingSet.proto GatingSet_pb2.py
These are unlikely file names for src files.
* 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 ‘cytolib’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 16.9Mb
  sub-directories of 1Mb or more:
    lib   13.3Mb
    libs   2.4Mb
* 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 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 C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘cytolib/libs/cytolib.so’:
  Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
    Objects: ‘GatingHierarchy.o’, ‘GatingSet.o’, ‘gate.o’,
      ‘nodeProperties.o’, ‘transformation.o’

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.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/cytolib.Rcheck/00check.log’
for details.



Installation output

cytolib.Rcheck/00install.out

* installing *source* package ‘cytolib’ ...
** libs
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I../inst/include/ -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c GatingHierarchy.cpp -o GatingHierarchy.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I../inst/include/ -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c GatingSet.cpp -o GatingSet.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I../inst/include/ -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c GatingSet.pb.cc -o GatingSet.pb.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I../inst/include/ -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c POPINDICES.cpp -o POPINDICES.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I../inst/include/ -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c calibrationTable.cpp -o calibrationTable.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I../inst/include/ -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c compensation.cpp -o compensation.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I../inst/include/ -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c delimitedMessage.cpp -o delimitedMessage.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I../inst/include/ -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c ellipse2points.cpp -o ellipse2points.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I../inst/include/ -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c flowData.cpp -o flowData.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I../inst/include/ -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c gate.cpp -o gate.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I../inst/include/ -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c global.cpp -o global.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I../inst/include/ -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c nodeProperties.cpp -o nodeProperties.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I../inst/include/ -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c spline.cpp -o spline.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I../inst/include/ -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c transformation.cpp -o transformation.o
transformation.cpp:273:68: warning: field 'T' will be initialized after field 'scale' [-Wreorder]
logTrans::logTrans():transformation(false,LOG),offset(0),decade(1),T(262144), scale(1){
                                                                   ^
transformation.cpp:281:57: warning: field 'length' will be initialized after field 'maxRange' [-Wreorder]
fasinhTrans::fasinhTrans():transformation(false,FASINH),length(256),maxRange(262144), T(262144),A(0),M(4.5){
                                                        ^
2 warnings generated.
mkdir -p "/Users/biocbuild/bbs-3.6-bioc/meat/cytolib.Rcheck/cytolib/lib"
ar rs "/Users/biocbuild/bbs-3.6-bioc/meat/cytolib.Rcheck/cytolib/lib/libcytolib.a" GatingHierarchy.o GatingSet.o GatingSet.pb.o POPINDICES.o calibrationTable.o compensation.o delimitedMessage.o ellipse2points.o flowData.o gate.o global.o nodeProperties.o spline.o transformation.o
ar: creating archive /Users/biocbuild/bbs-3.6-bioc/meat/cytolib.Rcheck/cytolib/lib/libcytolib.a
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o cytolib.so GatingHierarchy.o GatingSet.o GatingSet.pb.o POPINDICES.o calibrationTable.o compensation.o delimitedMessage.o ellipse2points.o flowData.o gate.o global.o nodeProperties.o spline.o transformation.o /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/lib/libprotobuf.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-bioc/meat/cytolib.Rcheck/cytolib/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (cytolib)

Tests output


Example timings

cytolib.Rcheck/cytolib-Ex.timings

nameusersystemelapsed
LdFlags0.0360.0010.037