bgx 1.34.0
Ernest Turro
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/bgx | | Last Changed Rev: 102591 / Revision: 109384 | | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings bgx_1.34.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/bgx.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bgx/DESCRIPTION’ ... OK
* this is package ‘bgx’ version ‘1.34.0’
* 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 ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘bgx’ can be installed ... [21s/24s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
‘Biobase’ ‘affy’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
bgx: no visible global function definition for ‘geneNames’
bgx: no visible global function definition for ‘sampleNames’
bgx: no visible global function definition for ‘annotation’
bgx: no visible global function definition for ‘description’
bgx: no visible global function definition for
‘assayDataElementReplace’
setupVars.bgx : calcProbeAffCategories: no visible global function
definition for ‘cdfName’
setupVars.bgx: no visible global function definition for ‘pData’
setupVars.bgx: no visible global function definition for ‘indexProbes’
standalone.bgx: no visible global function definition for ‘geneNames’
standalone.bgx: no visible global function definition for ‘sampleNames’
* checking Rd files ... NOTE
prepare_Rd: analysis.bgx.Rd:48-49: Dropping empty section \examples
prepare_Rd: mcmc.bgx.Rd:48-49: Dropping empty section \examples
prepare_Rd: readOutput.bgx.Rd:23-24: Dropping empty section \examples
prepare_Rd: saveAffinityPlot.bgx.Rd:18-19: Dropping empty section \details
prepare_Rd: saveAffinityPlot.bgx.Rd:20-21: Dropping empty section \value
prepare_Rd: saveAffinityPlot.bgx.Rd:26-27: Dropping empty section \examples
prepare_Rd: setupVars.bgx.Rd:21-22: Dropping empty section \details
prepare_Rd: setupVars.bgx.Rd:43-44: Dropping empty section \examples
* 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 ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work. If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it. If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [28s/35s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
bgx 23.345 1.343 31.513
* 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: 5 NOTEs
See
‘/Users/biocbuild/bbs-3.1-bioc/meat/bgx.Rcheck/00check.log’
for details.
* installing *source* package ‘bgx’ ...
checking for gcc... clang
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking for C compiler vendor... gnu
checking whether C compiler accepts -ffast-math... yes
checking whether C compiler accepts -O3... yes
checking build system type... i386-apple-darwin13.4.0
checking host system type... i386-apple-darwin13.4.0
checking for gcc architecture flag...
checking for x86 cpuid 0 output... d:756e6547:6c65746e:49656e69
checking for x86 cpuid 1 output... 306a9:3100800:7fbae3ff:bfebfbff
checking whether C compiler accepts -march=pentium2... no
checking whether C compiler accepts -mcpu=pentium2... yes
checking for gcc architecture flag... -mcpu=pentium2
checking for clang option to accept ISO C99... none needed
checking for main in -lm... yes
Untarring Boost header files...
checking for an ANSI C-conforming const... yes
checking for inline... inline
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I ../boostIncl -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -ffast-math -O3 -DUSING_R -c bgx.cc -o bgx.o
In file included from bgx.cc:29:
./bgx_updates.hh:47:8: warning: private field 'categories' is not used [-Wunused-private-field]
int* categories;
^
./bgx_updates.hh:310:8: warning: private field 'categories' is not used [-Wunused-private-field]
int *categories;
^
./bgx_updates.hh:311:7: warning: private field 'numberCategories' is not used [-Wunused-private-field]
int numberCategories;
^
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I ../boostIncl -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -ffast-math -O3 -DUSING_R -c bgx_frontend.cc -o bgx_frontend.o
bgx_frontend.cc:251:16: warning: comparison between NULL and non-pointer ('int' and NULL) [-Wnull-arithmetic]
if(SampleSets==NULL){
˜˜˜˜˜˜˜˜˜˜^ ˜˜˜˜
bgx_frontend.cc:261:15: warning: comparison between NULL and non-pointer ('int' and NULL) [-Wnull-arithmetic]
if(ProbeSets==NULL){
˜˜˜˜˜˜˜˜˜^ ˜˜˜˜
bgx_frontend.cc:271:16: warning: comparison between NULL and non-pointer ('int' and NULL) [-Wnull-arithmetic]
if(Categories==NULL){
˜˜˜˜˜˜˜˜˜˜^ ˜˜˜˜
bgx_frontend.cc:281:22: warning: comparison between NULL and non-pointer ('int' and NULL) [-Wnull-arithmetic]
if(UnknownProbeSeqs==NULL){
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^ ˜˜˜˜
bgx_frontend.cc:291:18: warning: comparison between NULL and non-pointer ('int' and NULL) [-Wnull-arithmetic]
if(GenesToWatch==NULL){
˜˜˜˜˜˜˜˜˜˜˜˜^ ˜˜˜˜
bgx_frontend.cc:301:33: warning: comparison between NULL and non-pointer ('int' and NULL) [-Wnull-arithmetic]
if(FirstProbeInEachGeneToWatch==NULL){
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^ ˜˜˜˜
bgx_frontend.cc:311:8: warning: comparison between NULL and non-pointer ('int' and NULL) [-Wnull-arithmetic]
if(PM==NULL){
˜˜^ ˜˜˜˜
bgx_frontend.cc:316:8: warning: comparison between NULL and non-pointer ('int' and NULL) [-Wnull-arithmetic]
if(MM==NULL){
˜˜^ ˜˜˜˜
8 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I ../boostIncl -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -g -O2 -mcpu=pentium2 -ffast-math -O3 -c qnorm.c -o qnorm.o
clang: warning: argument unused during compilation: '-mcpu=pentium2'
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I ../boostIncl -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -ffast-math -O3 -DUSING_R -c rundir.cc -o rundir.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I ../boostIncl -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -ffast-math -O3 -DUSING_R -c sokal.cc -o sokal.o
clang++ -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 bgx.so bgx.o bgx_frontend.o qnorm.o rundir.o sokal.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
rm -r ../boostIncl
installing to /Users/biocbuild/bbs-3.1-bioc/meat/bgx.Rcheck/bgx/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (bgx)