specL 1.3.5
Christian Panse , Witold E. Wolski
| Snapshot Date: 2015-08-19 16:24:33 -0700 (Wed, 19 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/specL | | Last Changed Rev: 107343 / Revision: 107602 | | Last Changed Date: 2015-08-12 05:35:51 -0700 (Wed, 12 Aug 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ WARNINGS ] | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | ERROR | skipped | skipped | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf specL.buildbin-libdir specL.Rcheck && mkdir specL.buildbin-libdir specL.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=specL.buildbin-libdir specL_1.3.5.tar.gz >specL.Rcheck\00install.out 2>&1 && cp specL.Rcheck\00install.out specL-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=specL.buildbin-libdir --install="check:specL-install.out" --force-multiarch --no-vignettes --timings specL_1.3.5.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/specL.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'specL/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'specL' version '1.3.5'
* 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 'specL' 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 ... WARNING
'library' or 'require' call not declared from: 'parallel'
'library' or 'require' calls in package code:
'BiocParallel' 'parallel'
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
'.decompose_intensity' '.decompose_peakMZ'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.convert_blib2psm_parallel: no visible global function definition for
'mcmapply'
.retentiontimePlot: no visible binding for global variable
'iRTpeptides'
plot,specLSet : .local: no visible global function definition for
'draw.circle'
summary,specLSet : .local : <anonymous>: no visible binding for global
variable 'iRTpeptides'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'annotate.protein_id':
annotate.protein_id
Code: function(data, file = NULL, fasta = read.fasta(file = file,
as.string = TRUE, seqtype = "AA"), digestPattern =
"(([RK])|(^)|(^M))", ncores = parallel::detectCores())
Docs: function(data, file = NULL, fasta = read.fasta(file = file,
as.string = TRUE, seqtype = "AA"), digestPattern =
"(([RK])|(^)|(^M))")
Argument names in code not in docs:
ncores
Codoc mismatches from documentation object 'read.bibliospec':
read.bibliospec
Code: function(file, ncores = NULL)
Docs: function(file)
Argument names in code not in docs:
ncores
* 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/specL.buildbin-libdir/specL/libs/i386/specL.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-3.2-bioc/meat/specL.buildbin-libdir/specL/libs/x64/specL.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 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' ... [19s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
genSwathIonLib 1.04 0.39 15.88
** running examples for arch 'x64' ... [20s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
genSwathIonLib 0.95 0.63 18.3
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R' [159s]
[160s] OK
** running tests for arch 'x64' ...
Running 'runTests.R' [178s]
[178s] 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: 2 WARNINGs, 2 NOTEs
See
'D:/biocbld/bbs-3.2-bioc/meat/specL.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'specL' ...
** libs
g++ -m32 -std=c++0x -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/local320/include" -O2 -Wall -mtune=core2 -c lower_bound.cpp -o lower_bound.o
g++ -m32 -shared -s -static-libgcc -o specL.dll tmp.def lower_bound.o -Ld:/RCompile/r-compiling/local/local320/lib/i386 -Ld:/RCompile/r-compiling/local/local320/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.2-bioc/meat/specL.buildbin-libdir/specL/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in package 'specL'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'specL' ...
** libs
g++ -m64 -std=c++0x -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/local320/include" -O2 -Wall -mtune=core2 -c lower_bound.cpp -o lower_bound.o
g++ -m64 -shared -s -static-libgcc -o specL.dll tmp.def lower_bound.o -Ld:/RCompile/r-compiling/local/local320/lib/x64 -Ld:/RCompile/r-compiling/local/local320/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.2-bioc/meat/specL.buildbin-libdir/specL/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'specL' as specL_1.3.5.zip
* DONE (specL)