BioC 2.13: CHECK report for casper on moscato1
This page was generated on 2014-04-05 09:51:11 -0700 (Sat, 05 Apr 2014).
casper 1.4.0
David Rossell
| Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/casper | | Last Changed Rev: 81642 / Revision: 88450 | | Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | WARNINGS | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | [ WARNINGS ] | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | WARNINGS | OK |
Summary
| Package: casper
|
| Version: 1.4.0
|
| Command: rm -rf casper.buildbin-libdir && mkdir casper.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=casper.buildbin-libdir casper_1.4.0.tar.gz >casper-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=casper.buildbin-libdir --install="check:casper-install.out" --force-multiarch --no-vignettes --timings casper_1.4.0.tar.gz && mv casper.buildbin-libdir/* casper.Rcheck/ && rmdir casper.buildbin-libdir
|
| StartedAt: 2014-04-05 02:46:25 -0700 (Sat, 05 Apr 2014)
|
| EndedAt: 2014-04-05 02:55:25 -0700 (Sat, 05 Apr 2014)
|
| EllapsedTime: 539.8 seconds
|
| RetCode: 0
|
| Status: WARNINGS
|
| CheckDir: casper.Rcheck
|
| Warnings: 3
|
Command output
* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/casper.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'casper/DESCRIPTION' ... OK
* this is package 'casper' version '1.4.0'
* 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 'casper' 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
* 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 dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
'IRanges' 'gaga' 'plyr'
Please remove these calls from your code.
Packages in Depends field not imported from:
'Biobase' 'GenomicRanges' 'Rsamtools' 'gaga' 'gtools' 'methods'
'plyr'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
':::' call which should be '::': 'parallel:::mclapply'
See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
'GenomicFeatures:::.prepareGTFTables' 'gaga:::groups2int'
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
'calcKnownMultiple' 'makeIslands' 'mergeDisWr' 'mergeGRanges'
'mergePCWr' 'qtnorm' 'splitPaths'
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* 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 ... WARNING
Undocumented S4 methods:
generic '[[' and siglist 'denovoGenomeExpr,ANY,ANY'
generic 'coef' and siglist 'modelPriorAS'
generic 'txLength' and siglist 'missing,data.frame,annotatedGenome'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'calcDenovo':
calcDenovo
Code: function(distrs, genomeDB, pc, readLength, islandid, priorq =
3, mprior, minpp = 0.001, selectBest = FALSE, method =
"auto", niter, exactMarginal = TRUE, integrateMethod =
"plugin", verbose = TRUE, mc.cores = 1)
Docs: function(distrs, genomeDB, pc, readLength, islandid, priorq =
3, mprior, minpp = 0.001, selectBest = FALSE, method =
"auto", niter, exactMarginal = TRUE, verbose = TRUE,
mc.cores = 1)
Argument names in code not in docs:
integrateMethod
Mismatches in argument names:
Position: 13 Code: integrateMethod Docs: verbose
Position: 14 Code: verbose Docs: mc.cores
Codoc mismatches from documentation object 'denovoExpr':
denovoExpr
Code: function(x, pc, rpkm = TRUE, summarize = "modelAvg",
minProbExpr = 0.5, minExpr = 0.05)
Docs: function(x, pc, rpkm = TRUE, summarize = "modelAvg",
minProbExpr = 0.5, minExpr = 0)
Mismatches in argument default values:
Name: 'minExpr' Code: 0.05 Docs: 0
S4 class codoc mismatches from documentation object 'annotatedGenome-class':
Slots for class 'annotatedGenome'
Code: aliases dateCreated denovo exon2island exonsNI genomeVersion
islands knownVars transcripts txLength
Docs: aliases dateCreated denovo exon2island exonsNI genomeVersion
islands transcripts txLength
* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'calcDenovo':
'integrateMethod'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 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-2.13-bioc/meat/casper.buildbin-libdir/casper/libs/i386/casper.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-2.13-bioc/meat/casper.buildbin-libdir/casper/libs/x64/casper.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. 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' ... [38s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
denovoExpr 5.71 0.10 6.78
calcExp 5.60 0.14 5.74
** running examples for arch 'x64' ... [40s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
denovoExpr 6.47 0.23 7.34
calcExp 6.23 0.22 6.44
* 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
WARNING: There were 3 warnings.
NOTE: There were 2 notes.
See
'D:/biocbld/bbs-2.13-bioc/meat/casper.Rcheck/00check.log'
for details.
casper.Rcheck/00install.out:
install for i386
* installing *source* package 'casper' ...
** libs
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c casper.cpp -o casper.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c cstat.cpp -o cstat.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c dataframe.cpp -o dataframe.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c discretedf.cpp -o discretedf.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c dropVariant.cpp -o dropVariant.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c exon.cpp -o exon.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c fragFunc.c -o fragFunc.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c fragment.cpp -o fragment.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c functions.c -o functions.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c hash.c -o hash.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c join_exons.c -o join_exons.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c makeIslands.c -o makeIslands.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c model.cpp -o model.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c model_cmp.cpp -o model_cmp.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c pathCounts.c -o pathCounts.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c procBam.c -o procBam.o
procBam.c: In function 'procBam':
procBam.c:15:43: warning: variable 'reads_size' set but not used [-Wunused-but-set-variable]
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c rcasper.cpp -o rcasper.o
rcasper.cpp: In function 'SEXPREC* calcDenovoSingle(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
rcasper.cpp:1145:17: warning: 'bestModel' may be used uninitialized in this function [-Wuninitialized]
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c seppel.cpp -o seppel.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c simReads.c -o simReads.o
simReads.c: In function 'casperSimC':
simReads.c:146:36: warning: 'cigars' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c simReadsfunc.c -o simReadsfunc.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c smartmodeldist.cpp -o smartmodeldist.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c uniqQname.c -o uniqQname.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c variant.cpp -o variant.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c variant_cmp.cpp -o variant_cmp.o
g++ -m32 -shared -s -static-libgcc -o casper.dll tmp.def casper.o cstat.o dataframe.o discretedf.o dropVariant.o exon.o fragFunc.o fragment.o functions.o hash.o join_exons.o makeIslands.o model.o model_cmp.o pathCounts.o procBam.o rcasper.o seppel.o simReads.o simReadsfunc.o smartmodeldist.o uniqQname.o variant.o variant_cmp.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.13-/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.13-bioc/meat/casper.buildbin-libdir/casper/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for 'transcripts' in package 'casper'
Creating a generic function for 'coef' from package 'stats' in package 'casper'
Creating a generic function for 'plot' from package 'graphics' in package 'casper'
Creating a generic function for 'lines' from package 'graphics' in package 'casper'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'casper' ...
** libs
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c casper.cpp -o casper.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c cstat.cpp -o cstat.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c dataframe.cpp -o dataframe.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c discretedf.cpp -o discretedf.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c dropVariant.cpp -o dropVariant.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c exon.cpp -o exon.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c fragFunc.c -o fragFunc.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c fragment.cpp -o fragment.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c functions.c -o functions.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c hash.c -o hash.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c join_exons.c -o join_exons.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c makeIslands.c -o makeIslands.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c model.cpp -o model.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c model_cmp.cpp -o model_cmp.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c pathCounts.c -o pathCounts.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c procBam.c -o procBam.o
procBam.c: In function 'procBam':
procBam.c:15:43: warning: variable 'reads_size' set but not used [-Wunused-but-set-variable]
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c rcasper.cpp -o rcasper.o
rcasper.cpp: In function 'SEXPREC* calcDenovoSingle(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
rcasper.cpp:1145:17: warning: 'bestModel' may be used uninitialized in this function [-Wuninitialized]
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c seppel.cpp -o seppel.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c simReads.c -o simReads.o
simReads.c: In function 'casperSimC':
simReads.c:146:36: warning: 'cigars' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c simReadsfunc.c -o simReadsfunc.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c smartmodeldist.cpp -o smartmodeldist.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c uniqQname.c -o uniqQname.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c variant.cpp -o variant.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c variant_cmp.cpp -o variant_cmp.o
g++ -m64 -shared -s -static-libgcc -o casper.dll tmp.def casper.o cstat.o dataframe.o discretedf.o dropVariant.o exon.o fragFunc.o fragment.o functions.o hash.o join_exons.o makeIslands.o model.o model_cmp.o pathCounts.o procBam.o rcasper.o seppel.o simReads.o simReadsfunc.o smartmodeldist.o uniqQname.o variant.o variant_cmp.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.13-/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.13-bioc/meat/casper.buildbin-libdir/casper/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'casper' as casper_1.4.0.zip
* DONE (casper)
casper.Rcheck/examples_i386/casper-Ex.timings:
| name | user | system | elapsed
|
| K562.r1l1 | 0.25 | 0.03 | 0.28 |
|
| annotatedGenome-class | 0 | 0 | 0 |
|
| calcDenovo | 0 | 0 | 0 |
|
| calcExp | 5.60 | 0.14 | 5.74 |
|
| denovoExpr | 5.71 | 0.10 | 6.78 |
|
| denovoGeneExpr-class | 0.02 | 0.00 | 0.01 |
|
| denovoGenomeExpr-class | 0.01 | 0.00 | 0.02 |
|
| genePlot | 1.83 | 0.00 | 1.82 |
|
| getDistrs | 1.46 | 0.04 | 1.52 |
|
| getIsland | 0.29 | 0.00 | 1.27 |
|
| getNreads | 0.36 | 0.00 | 0.36 |
|
| getReads | 0 | 0 | 0 |
|
| getRoc | 0 | 0 | 0 |
|
| hg19DB | 0.21 | 0.00 | 0.20 |
|
| mergeBatches | 0.26 | 0.00 | 0.26 |
|
| mergeExp | 0 | 0 | 0 |
|
| modelPrior | 0.72 | 0.00 | 0.72 |
|
| modelPriorAS-class | 0 | 0 | 0 |
|
| pathCounts-class | 0 | 0 | 0 |
|
| pathCounts | 0 | 0 | 0 |
|
| plot-methods | 0 | 0 | 0 |
|
| plotExpr | 0 | 0 | 0 |
|
| plotPriorAS | 0 | 0 | 0 |
|
| probNonEquiv | 0.35 | 0.02 | 1.80 |
|
| procBam-class | 0.01 | 0.00 | 0.01 |
|
| procBam | 0.02 | 0.00 | 0.02 |
|
| procGenome | 0.01 | 0.00 | 0.02 |
|
| rmShortInserts | 0.02 | 0.00 | 0.01 |
|
| simReads | 1.72 | 0.08 | 1.80 |
|
| simulatedSamples-class | 0.01 | 0.00 | 0.01 |
|
| splitGenomeByLength | 0.02 | 0.00 | 0.02 |
|
| transcripts | 0.9 | 0.0 | 0.9 |
|
| wrapKnown | 0.02 | 0.00 | 0.02 |
|
casper.Rcheck/examples_x64/casper-Ex.timings:
| name | user | system | elapsed
|
| K562.r1l1 | 0.26 | 0.04 | 0.31 |
|
| annotatedGenome-class | 0 | 0 | 0 |
|
| calcDenovo | 0 | 0 | 0 |
|
| calcExp | 6.23 | 0.22 | 6.44 |
|
| denovoExpr | 6.47 | 0.23 | 7.34 |
|
| denovoGeneExpr-class | 0 | 0 | 0 |
|
| denovoGenomeExpr-class | 0.00 | 0.02 | 0.01 |
|
| genePlot | 2.42 | 0.03 | 3.31 |
|
| getDistrs | 1.80 | 0.04 | 1.84 |
|
| getIsland | 0.10 | 0.02 | 0.11 |
|
| getNreads | 0 | 0 | 0 |
|
| getReads | 0.02 | 0.00 | 0.01 |
|
| getRoc | 0 | 0 | 0 |
|
| hg19DB | 0.11 | 0.00 | 0.11 |
|
| mergeBatches | 0.22 | 0.00 | 0.22 |
|
| mergeExp | 0 | 0 | 0 |
|
| modelPrior | 0.60 | 0.00 | 2.15 |
|
| modelPriorAS-class | 0.01 | 0.00 | 0.02 |
|
| pathCounts-class | 0.02 | 0.00 | 0.01 |
|
| pathCounts | 0.02 | 0.00 | 0.02 |
|
| plot-methods | 0 | 0 | 0 |
|
| plotExpr | 0 | 0 | 0 |
|
| plotPriorAS | 0.02 | 0.00 | 0.02 |
|
| probNonEquiv | 0.37 | 0.00 | 0.37 |
|
| procBam-class | 0 | 0 | 0 |
|
| procBam | 0 | 0 | 0 |
|
| procGenome | 0 | 0 | 0 |
|
| rmShortInserts | 0 | 0 | 0 |
|
| simReads | 1.68 | 0.03 | 1.72 |
|
| simulatedSamples-class | 0 | 0 | 0 |
|
| splitGenomeByLength | 0.01 | 0.00 | 0.02 |
|
| transcripts | 1.10 | 0.00 | 1.09 |
|
| wrapKnown | 0.03 | 0.00 | 0.03 |
|