Multiple platform build/check report for BioC 3.6 - CHECK report for spliceSites on tokay1

Package: spliceSites

Version: 1.26.0

Command: rm -rf spliceSites.buildbin-libdir spliceSites.Rcheck && mkdir spliceSites.buildbin-libdir spliceSites.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=spliceSites.buildbin-libdir spliceSites_1.26.0.tar.gz >spliceSites.Rcheck\00install.out 2>&1 && cp spliceSites.Rcheck\00install.out spliceSites-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=spliceSites.buildbin-libdir --install="check:spliceSites-install.out" --force-multiarch --no-vignettes --timings spliceSites_1.26.0.tar.gz

StartedAt: 2018-04-12 03:22:23 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 03:25:46 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 202.4 seconds

RetCode: 0

Status: OK

CheckDir: spliceSites.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf spliceSites.buildbin-libdir spliceSites.Rcheck && mkdir spliceSites.buildbin-libdir spliceSites.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=spliceSites.buildbin-libdir spliceSites_1.26.0.tar.gz >spliceSites.Rcheck\00install.out 2>&1 && cp spliceSites.Rcheck\00install.out spliceSites-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=spliceSites.buildbin-libdir --install="check:spliceSites-install.out" --force-multiarch --no-vignettes --timings spliceSites_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/spliceSites.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'spliceSites/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'spliceSites' version '1.26.0'
* 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 'spliceSites' can be installed ... OK
* checking installed package size ... OK
* 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 ... 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 ... 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 'C:/Users/biocbuild/bbs-3.6-bioc/meat/spliceSites.buildbin-libdir/spliceSites/libs/i386/spliceSites.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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/spliceSites.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'spliceSites' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c spliceSites.c -o spliceSites.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o spliceSites.dll tmp.def spliceSites.o -lm -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/spliceSites.buildbin-libdir/spliceSites/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'spliceSites'
    finding HTML links ... done
    SpliceCountSet-class                    html  
    aaGapSites-class                        html  
    addGeneAligns                           html  
    addGenomeData-ExpressionSet             html  
    addGenomeData-gapSites                  html  
    addHbond                                html  
    addMaxEnt                               html  
    alt_X_ranks                             html  
    annGapSites-class                       html  
    annotate-ExpressionSet                  html  
    annotation                              html  
    as.data.frame-methods                   html  
    c-methods                               html  
    cRanges-class                           html  
    caRanges-class                          html  
    cdRanges-class                          html  
    countByGeneName                         html  
    dim-methods                             html  
    dnaGapSites-class                       html  
    dnaRanges                               html  
    extractByGeneName                       html  
    extractRange                            html  
    gapSites-class                          html  
    gapSites                                html  
    getGapSites                             html  
    hbond-class                             html  
    head-methods                            html  
    initialize-methods                      html  
    keyProfiler-class                       html  
    lrCodons                                html  
    maxEnt-class                            html  
    merge-methods                           html  
    plotGeneAlignDepth                      html  
    rangeByGeneName                         html  
    readCuffGeneFpkm                        html  
    readExpSet                              html  
    readMergedBamGaps                       html  
    readTabledBamGaps                       html  
    seqlogo                                 html  
    silic_tryp                              html  
    sortTable-methods                       html  
    spliceSites-package                     html  
    trim                                    html  
    truncateSeq                             html  
    truncate_seq                            html  
    trypsinCleave                           html  
    uniqueJuncAnn                           html  
    write.files                             html  
    xCodons                                 html  
    xJunc                                   html  
    xJuncStrand                             html  
    z[-methods                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'spliceSites' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c spliceSites.c -o spliceSites.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o spliceSites.dll tmp.def spliceSites.o -lm -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/spliceSites.buildbin-libdir/spliceSites/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'spliceSites' as spliceSites_1.26.0.zip
* DONE (spliceSites)
In R CMD INSTALL
In R CMD INSTALL

name	user	system	elapsed
SpliceCountSet-class	0	0	0
aaGapSites-class	0.41	0.00	0.47
addGeneAligns	0.08	0.00	0.19
addGenomeData-ExpressionSet	0.7	0.0	0.7
addGenomeData-gapSites	0.60	0.03	0.62
addHbond	0.12	0.00	0.13
addMaxEnt	0.13	0.02	0.14
alt_X_ranks	0.03	0.00	0.03
annGapSites-class	0.06	0.00	0.06
annotate-ExpressionSet	0.22	0.00	0.22
annotation	0.03	0.00	0.03
cRanges-class	0.05	0.00	0.05
caRanges-class	0.09	0.00	0.09
cdRanges-class	0.56	0.02	0.58
countByGeneName	0.25	0.00	0.25
dnaGapSites-class	0.19	0.00	0.18
dnaRanges	0.48	0.01	0.50
extractByGeneName	0.14	0.00	0.15
extractRange	0.03	0.00	0.03
gapSites-class	0.05	0.00	0.04
gapSites	0.08	0.00	0.08
getGapSites	0.05	0.00	0.05
hbond-class	0.01	0.00	0.01
keyProfiler-class	0.03	0.00	0.04
lrCodons	0.03	0.00	0.03
maxEnt-class	0.04	0.00	0.03
plotGeneAlignDepth	0.09	0.00	0.09
rangeByGeneName	0.01	0.00	0.02
readCuffGeneFpkm	0.05	0.00	0.04
readExpSet	0.04	0.00	0.05
readMergedBamGaps	0.08	0.00	0.07
readTabledBamGaps	0.13	0.00	0.13
seqlogo	0.11	0.00	0.11
silic_tryp	0	0	0
spliceSites-package	0.04	0.00	0.05
trim	0.03	0.00	0.03
truncateSeq	0.08	0.00	0.08
truncate_seq	0	0	0
trypsinCleave	0.07	0.00	0.06
uniqueJuncAnn	0.10	0.00	0.11
write.files	0.05	0.02	0.06
xCodons	0.05	0.01	0.06
xJunc	0.01	0.00	0.02
xJuncStrand	0.07	0.00	0.06

name	user	system	elapsed
SpliceCountSet-class	0	0	0
aaGapSites-class	0.47	0.00	0.53
addGeneAligns	0.09	0.00	0.12
addGenomeData-ExpressionSet	1.06	0.03	1.10
addGenomeData-gapSites	0.44	0.02	0.45
addHbond	0.49	0.00	0.48
addMaxEnt	0.17	0.02	0.19
alt_X_ranks	0.01	0.00	0.02
annGapSites-class	0.07	0.00	0.06
annotate-ExpressionSet	0.28	0.00	0.28
annotation	0.01	0.00	0.02
cRanges-class	0.05	0.00	0.04
caRanges-class	0.13	0.00	0.13
cdRanges-class	0.76	0.01	0.78
countByGeneName	0.31	0.00	0.31
dnaGapSites-class	0.24	0.00	0.24
dnaRanges	0.33	0.02	0.34
extractByGeneName	0.17	0.00	0.17
extractRange	0.04	0.00	0.05
gapSites-class	0.04	0.00	0.03
gapSites	0.07	0.01	0.09
getGapSites	0.05	0.00	0.05
hbond-class	0.02	0.02	0.03
keyProfiler-class	0.03	0.00	0.03
lrCodons	0.04	0.00	0.05
maxEnt-class	0.04	0.00	0.03
plotGeneAlignDepth	0.07	0.01	0.10
rangeByGeneName	0.04	0.00	0.03
readCuffGeneFpkm	0.04	0.00	0.04
readExpSet	0.06	0.02	0.08
readMergedBamGaps	0.1	0.0	0.1
readTabledBamGaps	0.17	0.00	0.17
seqlogo	0.11	0.00	0.11
silic_tryp	0	0	0
spliceSites-package	0.03	0.00	0.03
trim	0.03	0.00	0.04
truncateSeq	0.08	0.02	0.09
truncate_seq	0	0	0
trypsinCleave	0.06	0.01	0.08
uniqueJuncAnn	0.13	0.00	0.13
write.files	0.06	0.00	0.06
xCodons	0.03	0.02	0.05
xJunc	0.01	0.00	0.02
xJuncStrand	0.07	0.00	0.06

CHECK report for spliceSites on tokay1

Summary

Command output

Installation output

Tests output

Example timings