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) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:45:30 -0400 (Thu, 12 Apr 2018).
| Package 324/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| cytolib 1.0.1 Mike Jiang
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| 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 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cytolib_1.0.1.tar.gz
###
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* 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.
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)
cytolib.Rcheck/cytolib-Ex.timings
| name | user | system | elapsed | |
| LdFlags | 0.036 | 0.001 | 0.037 | |