R3CPET 1.2.0
Mohamed Nadhir Djekidel
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/R3CPET | | Last Changed Rev: 109589 / Revision: 116712 | | Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | [ WARNINGS ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
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### Running command:
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### rm -rf R3CPET.buildbin-libdir R3CPET.Rcheck && mkdir R3CPET.buildbin-libdir R3CPET.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=R3CPET.buildbin-libdir R3CPET_1.2.0.tar.gz >R3CPET.Rcheck\00install.out 2>&1 && cp R3CPET.Rcheck\00install.out R3CPET-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=R3CPET.buildbin-libdir --install="check:R3CPET-install.out" --force-multiarch --no-vignettes --timings R3CPET_1.2.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/R3CPET.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'R3CPET/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'R3CPET' version '1.2.0'
* 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 whether package 'R3CPET' can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.9Mb
sub-directories of 1Mb or more:
data 3.0Mb
example 1.0Mb
libs 1.3Mb
* 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
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 ... NOTE
.GetClusterInfo: no visible binding for global variable
'TxDb.Hsapiens.UCSC.hg19.knownGene'
.GetClusterInfo: no visible global function definition for 'toTable'
.GetClusterInfo: no visible binding for global variable
'org.Hs.egUCSCKG'
.GetClusterInfo: no visible global function definition for 'select'
.GetClusterInfo: no visible binding for global variable 'org.Hs.eg.db'
.formatDAVIDResult: no visible global function definition for
'formatGeneReportFull'
.formatDAVIDResult: no visible global function definition for
'formatGeneReport'
.formatDAVIDResult: no visible global function definition for
'formatList'
.formatDAVIDResult: no visible global function definition for
'formatGene2Gene'
.formatDAVIDResult: no visible global function definition for
'formatAnnotationReport'
.get.NetworksGenes: no visible global function definition for
'annotatePeakInBatch'
EnsemblToHGNC: no visible global function definition for 'useMart'
EnsemblToHGNC: no visible global function definition for 'useDataset'
EnsemblToHGNC: no visible global function definition for 'getBM'
EntrezToHGNC: no visible global function definition for 'useMart'
EntrezToHGNC: no visible global function definition for 'useDataset'
EntrezToHGNC: no visible global function definition for 'getBM'
createServer,ChiapetExperimentData-NetworkCollection-ChromMaintainers:
no visible global function definition for 'runApp'
plotTrack,ChiapetExperimentData-GRanges: no visible global function
definition for 'keepSeqlevels'
plotTrack,ChiapetExperimentData-GRanges: no visible global function
definition for 'seqlevels'
plotTrack,ChiapetExperimentData-GRanges: no visible global function
definition for 'seqlengths<-'
plotTrack,ChiapetExperimentData-GRanges: no visible global function
definition for 'seqlengths'
visualizeCircos,ChromMaintainers-ChiapetExperimentData-numeric :
.local: no visible global function definition for 'keepSeqlevels'
visualizeCircos,ChromMaintainers-ChiapetExperimentData-numeric :
.local: no visible global function definition for 'seqlevels'
visualizeCircos,ChromMaintainers-ChiapetExperimentData-numeric :
.local: no visible global function definition for 'seqlengths<-'
visualizeCircos,ChromMaintainers-ChiapetExperimentData-numeric :
.local: no visible global function definition for 'seqlengths'
visualizeInteractions,ChiapetExperimentData-GRanges: no visible global
function definition for 'keepSeqlevels'
visualizeInteractions,ChiapetExperimentData-GRanges: no visible global
function definition for 'seqlevels'
visualizeInteractions,ChiapetExperimentData-GRanges: no visible global
function definition for 'seqlengths<-'
visualizeInteractions,ChiapetExperimentData-GRanges: no visible global
function definition for 'seqlengths'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'plotRes-methods.Rd':
'ggplot2'
See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-3.2-bioc/meat/R3CPET.buildbin-libdir/R3CPET/libs/i386/R3CPET.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'rand', possibly from 'rand' (C)
File 'D:/biocbld/bbs-3.2-bioc/meat/R3CPET.buildbin-libdir/R3CPET/libs/x64/R3CPET.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'rand', possibly from 'rand' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [21s] OK
** running examples for arch 'x64' ... [27s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'tests.R' [0s]
[1s] OK
** running tests for arch 'x64' ...
Running 'tests.R' [1s]
[1s] 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
'D:/biocbld/bbs-3.2-bioc/meat/R3CPET.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'R3CPET' ...
** libs
gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c R3CPET_init.c -o R3CPET_init.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -mtune=core2 -c corpus.cpp -o corpus.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -mtune=core2 -c main.cpp -o main.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -mtune=core2 -c state.cpp -o state.o
state.cpp: In member function 'int HDP::sample_word_assignment(DocState*, int, bool, vct*)':
state.cpp:251:45: warning: 'k' may be used uninitialized in this function [-Wuninitialized]
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -mtune=core2 -c stirln.cpp -o stirln.o
g++ -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -mtune=core2 -c utils.cpp -o utils.o
g++ -m32 -shared -s -static-libgcc -o R3CPET.dll tmp.def R3CPET_init.o RcppExports.o corpus.o main.o state.o stirln.o utils.o -Ld:/RCompile/r-compiling/local/local323/lib/i386 -Ld:/RCompile/r-compiling/local/local323/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.2-bioc/meat/R3CPET.buildbin-libdir/R3CPET/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio'
No methods found in "GenomicRanges" for requests: seqlengths
No methods found in "GenomicRanges" for requests: keepSeqlevels
No methods found in "GenomicRanges" for requests: seqlevels
No methods found in "GenomicRanges" for requests: seqlengths<-
NOTE: arguments in definition for validity method for class 'ChromMaintainers' changed from (x) to (object)
NOTE: arguments in definition for validity method for class 'HLDAResult' changed from (x) to (object)
NOTE: arguments in definition for validity method for class 'NetworkCollection' changed from (x) to (object)
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio'
No methods found in "GenomicRanges" for requests: seqlengths
No methods found in "GenomicRanges" for requests: keepSeqlevels
No methods found in "GenomicRanges" for requests: seqlevels
No methods found in "GenomicRanges" for requests: seqlengths<-
install for x64
* installing *source* package 'R3CPET' ...
** libs
gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c R3CPET_init.c -o R3CPET_init.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -mtune=core2 -c corpus.cpp -o corpus.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -mtune=core2 -c main.cpp -o main.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -mtune=core2 -c state.cpp -o state.o
state.cpp: In member function 'int HDP::sample_word_assignment(DocState*, int, bool, vct*)':
state.cpp:251:45: warning: 'k' may be used uninitialized in this function [-Wuninitialized]
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -mtune=core2 -c stirln.cpp -o stirln.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"D:/biocbld/bbs-3.2-bioc/R/library/Rcpp/include" -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -mtune=core2 -c utils.cpp -o utils.o
g++ -m64 -shared -s -static-libgcc -o R3CPET.dll tmp.def R3CPET_init.o RcppExports.o corpus.o main.o state.o stirln.o utils.o -Ld:/RCompile/r-compiling/local/local323/lib/x64 -Ld:/RCompile/r-compiling/local/local323/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.2-bioc/meat/R3CPET.buildbin-libdir/R3CPET/libs/x64
** testing if installed package can be loaded
Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio'
No methods found in "GenomicRanges" for requests: seqlengths
No methods found in "GenomicRanges" for requests: keepSeqlevels
No methods found in "GenomicRanges" for requests: seqlevels
No methods found in "GenomicRanges" for requests: seqlengths<-
* MD5 sums
packaged installation of 'R3CPET' as R3CPET_1.2.0.zip
* DONE (R3CPET)