BioC 3.3: CHECK report for cn.mops on windows2.bioconductor.org
This page was generated on 2015-10-27 12:14:56 -0400 (Tue, 27 Oct 2015).
cn.mops 1.17.0
Guenter Klambauer
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/cn.mops | | Last Changed Rev: 109903 / Revision: 109948 | | Last Changed Date: 2015-10-25 07:55:33 -0400 (Sun, 25 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
Summary
| Package: cn.mops
|
| Version: 1.17.0
|
| Command: rm -rf cn.mops.buildbin-libdir cn.mops.Rcheck && mkdir cn.mops.buildbin-libdir cn.mops.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cn.mops.buildbin-libdir cn.mops_1.17.0.tar.gz >cn.mops.Rcheck\00install.out 2>&1 && cp cn.mops.Rcheck\00install.out cn.mops-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=cn.mops.buildbin-libdir --install="check:cn.mops-install.out" --force-multiarch --no-vignettes --timings cn.mops_1.17.0.tar.gz
|
| StartedAt: 2015-10-27 01:28:30 -0400 (Tue, 27 Oct 2015)
|
| EndedAt: 2015-10-27 01:34:13 -0400 (Tue, 27 Oct 2015)
|
| EllapsedTime: 342.7 seconds
|
| RetCode: 0
|
| Status: OK
|
| CheckDir: cn.mops.Rcheck
|
| Warnings: 0
|
Command output
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###
### Running command:
###
### rm -rf cn.mops.buildbin-libdir cn.mops.Rcheck && mkdir cn.mops.buildbin-libdir cn.mops.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cn.mops.buildbin-libdir cn.mops_1.17.0.tar.gz >cn.mops.Rcheck\00install.out 2>&1 && cp cn.mops.Rcheck\00install.out cn.mops-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=cn.mops.buildbin-libdir --install="check:cn.mops-install.out" --force-multiarch --no-vignettes --timings cn.mops_1.17.0.tar.gz
###
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/cn.mops.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cn.mops/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cn.mops' version '1.17.0'
* 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 'cn.mops' 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 ... NOTE
Warning: no function found corresponding to methods exports from 'cn.mops' for: 'sampleNames'
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
** 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 ... NOTE
Warning: no function found corresponding to methods exports from 'cn.mops' for: 'sampleNames'
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
** 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
'library' or 'require' call to 'DNAcopy' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'BiocGenerics'
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
.convertToFastSegRes: no visible global function definition for
'subjectHits'
.convertToFastSegRes: no visible global function definition for
'values<-'
.makeLogRatios: no visible global function definition for 'rowMedians'
.makeLogRatios: no visible global function definition for 'values<-'
.replaceNames: no visible global function definition for 'values<-'
.segPlot: no visible global function definition for 'seqnames'
.segPlot: no visible global function definition for 'ranges'
cn.mops: no visible global function definition for 'strand'
cn.mops: no visible global function definition for 'seqnames'
cn.mops: no visible global function definition for 'GRanges'
cn.mops: no visible global function definition for 'seqinfo'
cn.mops: no visible global function definition for 'sortSeqlevels'
cn.mops: no visible global function definition for 'reduce'
cn.mops: no visible global function definition for 'values<-'
getReadCountsFromBAM: no visible global function definition for
'sortSeqlevels'
getReadCountsFromBAM: no visible global function definition for
'seqlengths<-'
getReadCountsFromBAM: no visible global function definition for
'seqlevels'
haplocn.mops: no visible global function definition for 'strand'
haplocn.mops: no visible global function definition for 'seqnames'
haplocn.mops: no visible global function definition for 'GRanges'
haplocn.mops: no visible global function definition for 'seqinfo'
haplocn.mops: no visible global function definition for 'sortSeqlevels'
haplocn.mops: no visible global function definition for 'reduce'
normalizeChromosomes: no visible global function definition for
'seqnames'
normalizeChromosomes: no visible global function definition for
'values<-'
normalizeGenome: no visible global function definition for 'values<-'
referencecn.mops: no visible global function definition for 'strand'
referencecn.mops: no visible global function definition for 'seqnames'
referencecn.mops: no visible global function definition for 'GRanges'
referencecn.mops: no visible global function definition for 'seqinfo'
referencecn.mops: no visible global function definition for
'sortSeqlevels'
referencecn.mops: no visible global function definition for 'reduce'
referencecn.mops: no visible global function definition for 'values<-'
singlecn.mops: no visible global function definition for 'GRanges'
singlecn.mops: no visible global function definition for 'strand'
singlecn.mops: no visible global function definition for 'seqnames'
singlecn.mops: no visible global function definition for 'seqinfo'
singlecn.mops: no visible global function definition for
'sortSeqlevels'
calcIntegerCopyNumbers,CNVDetectionResult: no visible global function
definition for 'values<-'
individualCall,CNVDetectionResult: no visible global function
definition for 'values<-'
iniCall,CNVDetectionResult: no visible global function definition for
'values<-'
integerCopyNumber,CNVDetectionResult: no visible global function
definition for 'values<-'
localAssessments,CNVDetectionResult: no visible global function
definition for 'values<-'
makeRobustCNVR,CNVDetectionResult: no visible global function
definition for 'seqnames'
makeRobustCNVR,CNVDetectionResult: no visible global function
definition for 'GRanges'
makeRobustCNVR,CNVDetectionResult: no visible global function
definition for 'values<-'
makeRobustCNVR,CNVDetectionResult: no visible global function
definition for 'reduce'
normalizedData,CNVDetectionResult: no visible global function
definition for 'values<-'
plot,CNVDetectionResult-missing: no visible global function definition
for 'GRanges'
plot,CNVDetectionResult-missing: no visible global function definition
for 'seqnames'
plot,CNVDetectionResult-missing: no visible global function definition
for 'rowMedians'
segplot,CNVDetectionResult: no visible global function definition for
'sampleNames'
Undefined global functions or variables:
GRanges ranges reduce rowMedians sampleNames seqinfo seqlengths<-
seqlevels seqnames sortSeqlevels strand subjectHits values<-
* 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 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 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:/biocbld/bbs-3.3-bioc/meat/cn.mops.buildbin-libdir/cn.mops/libs/i386/cn.mops.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'c:/biocbld/bbs-3.3-bioc/meat/cn.mops.buildbin-libdir/cn.mops/libs/x64/cn.mops.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' ... [109s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
referencecn.mops 20.15 0.05 29.58
calcFractionalCopyNumbers-CNVDetectionResult-method 12.14 0.03 12.17
calcFractionalCopyNumbers 11.96 0.00 11.95
cn.mops 9.93 0.14 20.63
haplocn.mops 1.19 0.02 9.30
** running examples for arch 'x64' ... [109s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
referencecn.mops 15.99 0.03 26.22
cn.mops 11.40 0.11 23.11
calcFractionalCopyNumbers-CNVDetectionResult-method 10.30 0.04 10.33
calcFractionalCopyNumbers 10.01 0.01 10.03
haplocn.mops 1.61 0.01 10.55
* 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
'c:/biocbld/bbs-3.3-bioc/meat/cn.mops.Rcheck/00check.log'
for details.
cn.mops.Rcheck/00install.out:
install for i386
* installing *source* package 'cn.mops' ...
** libs
gcc -m32 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c R_init_cnmops.c -o R_init_cnmops.o
g++ -m32 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -mtune=core2 -c cnmops.cpp -o cnmops.o
g++ -m32 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -mtune=core2 -c segment.cpp -o segment.o
segment.cpp: In function 'SEXPREC* segment(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
segment.cpp:59:20: warning: variable 'globalSd' set but not used [-Wunused-but-set-variable]
segment.cpp:60:9: warning: variable 'oldStatistic' set but not used [-Wunused-but-set-variable]
segment.cpp:61:31: warning: variable 'maxStatistic' set but not used [-Wunused-but-set-variable]
segment.cpp:62:40: warning: variable 'maxIdx' set but not used [-Wunused-but-set-variable]
segment.cpp:64:9: warning: unused variable 'Rf_beta' [-Wunused-variable]
g++ -m32 -shared -s -static-libgcc -o cn.mops.dll tmp.def R_init_cnmops.o cnmops.o segment.o -Ld:/RCompile/r-compiling/local/local320/lib/i386 -Ld:/RCompile/r-compiling/local/local320/lib -Lc:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lR
installing to c:/biocbld/bbs-3.3-bioc/meat/cn.mops.buildbin-libdir/cn.mops/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'cn.mops' ...
** libs
gcc -m64 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c R_init_cnmops.c -o R_init_cnmops.o
g++ -m64 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -mtune=core2 -c cnmops.cpp -o cnmops.o
g++ -m64 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -mtune=core2 -c segment.cpp -o segment.o
segment.cpp: In function 'SEXPREC* segment(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
segment.cpp:59:20: warning: variable 'globalSd' set but not used [-Wunused-but-set-variable]
segment.cpp:60:9: warning: variable 'oldStatistic' set but not used [-Wunused-but-set-variable]
segment.cpp:61:31: warning: variable 'maxStatistic' set but not used [-Wunused-but-set-variable]
segment.cpp:62:40: warning: variable 'maxIdx' set but not used [-Wunused-but-set-variable]
segment.cpp:64:9: warning: unused variable 'Rf_beta' [-Wunused-variable]
g++ -m64 -shared -s -static-libgcc -o cn.mops.dll tmp.def R_init_cnmops.o cnmops.o segment.o -Ld:/RCompile/r-compiling/local/local320/lib/x64 -Ld:/RCompile/r-compiling/local/local320/lib -Lc:/biocbld/BBS-3˜1.3-B/R/bin/x64 -lR
installing to c:/biocbld/bbs-3.3-bioc/meat/cn.mops.buildbin-libdir/cn.mops/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cn.mops' as cn.mops_1.17.0.zip
* DONE (cn.mops)
cn.mops.Rcheck/examples_i386/cn.mops-Ex.timings:
| name | user | system | elapsed
|
| CNVDetectionResult | 0 | 0 | 0 |
|
| calcFractionalCopyNumbers-CNVDetectionResult-method | 12.14 | 0.03 | 12.17 |
|
| calcFractionalCopyNumbers | 11.96 | 0.00 | 11.95 |
|
| calcIntegerCopyNumbers-CNVDetectionResult-method | 0.33 | 0.02 | 0.35 |
|
| calcIntegerCopyNumbers | 0.32 | 0.00 | 0.32 |
|
| cn.mops | 9.93 | 0.14 | 20.63 |
|
| cnvr-CNVDetectionResult-method | 0.23 | 0.00 | 0.23 |
|
| cnvr | 0.23 | 0.00 | 0.24 |
|
| cnvs-CNVDetectionResult-method | 0.22 | 0.02 | 0.23 |
|
| cnvs | 0.22 | 0.00 | 0.22 |
|
| exomecn.mops | 4.08 | 0.00 | 4.08 |
|
| getReadCountsFromBAM | 0.09 | 0.03 | 3.98 |
|
| getSegmentReadCountsFromBAM | 0.07 | 0.00 | 3.83 |
|
| gr-CNVDetectionResult-method | 0.37 | 0.00 | 0.38 |
|
| gr | 0.25 | 0.01 | 0.26 |
|
| haplocn.mops | 1.19 | 0.02 | 9.30 |
|
| individualCall-CNVDetectionResult-method | 0.25 | 0.00 | 0.25 |
|
| individualCall | 0.22 | 0.01 | 0.23 |
|
| iniCall-CNVDetectionResult-method | 0.25 | 0.02 | 0.27 |
|
| iniCall | 0.23 | 0.00 | 0.23 |
|
| integerCopyNumber-CNVDetectionResult-method | 0.25 | 0.00 | 0.25 |
|
| integerCopyNumber | 0.25 | 0.00 | 0.25 |
|
| localAssessments-CNVDetectionResult-method | 0.23 | 0.01 | 0.25 |
|
| localAssessments | 0.24 | 0.02 | 0.25 |
|
| makeRobustCNVR | 0.36 | 0.00 | 0.35 |
|
| normalizeChromosomes | 0.28 | 0.00 | 0.29 |
|
| normalizeGenome | 0.5 | 0.0 | 0.5 |
|
| normalizedData-CNVDetectionResult-method | 0.25 | 0.00 | 0.25 |
|
| normalizedData | 0.23 | 0.00 | 0.23 |
|
| params-CNVDetectionResult-method | 0.22 | 0.01 | 0.23 |
|
| params | 0.24 | 0.00 | 0.24 |
|
| posteriorProbs-CNVDetectionResult-method | 0.23 | 0.00 | 0.23 |
|
| posteriorProbs | 0.22 | 0.02 | 0.24 |
|
| referencecn.mops | 20.15 | 0.05 | 29.58 |
|
| sampleNames-CNVDetectionResult-method | 0.22 | 0.01 | 0.23 |
|
| sampleNames | 0.24 | 0.00 | 0.23 |
|
| segment | 0.01 | 0.00 | 0.02 |
|
| segmentation-CNVDetectionResult-method | 0.25 | 0.00 | 0.25 |
|
| segmentation | 0.24 | 0.00 | 0.23 |
|
| segplot-CNVDetectionResult-method | 1.03 | 0.02 | 1.05 |
|
| segplot | 1.14 | 0.00 | 1.14 |
|
| singlecn.mops | 0.89 | 0.00 | 0.89 |
|
cn.mops.Rcheck/examples_x64/cn.mops-Ex.timings:
| name | user | system | elapsed
|
| CNVDetectionResult | 0.02 | 0.00 | 0.01 |
|
| calcFractionalCopyNumbers-CNVDetectionResult-method | 10.30 | 0.04 | 10.33 |
|
| calcFractionalCopyNumbers | 10.01 | 0.01 | 10.03 |
|
| calcIntegerCopyNumbers-CNVDetectionResult-method | 0.56 | 0.00 | 0.56 |
|
| calcIntegerCopyNumbers | 0.36 | 0.00 | 0.36 |
|
| cn.mops | 11.40 | 0.11 | 23.11 |
|
| cnvr-CNVDetectionResult-method | 0.25 | 0.02 | 0.26 |
|
| cnvr | 0.27 | 0.00 | 0.27 |
|
| cnvs-CNVDetectionResult-method | 0.27 | 0.00 | 0.27 |
|
| cnvs | 0.26 | 0.00 | 0.26 |
|
| exomecn.mops | 4.06 | 0.01 | 4.08 |
|
| getReadCountsFromBAM | 0.14 | 0.00 | 4.08 |
|
| getSegmentReadCountsFromBAM | 0.08 | 0.00 | 4.11 |
|
| gr-CNVDetectionResult-method | 0.33 | 0.02 | 0.34 |
|
| gr | 0.28 | 0.00 | 0.28 |
|
| haplocn.mops | 1.61 | 0.01 | 10.55 |
|
| individualCall-CNVDetectionResult-method | 0.45 | 0.03 | 0.48 |
|
| individualCall | 0.29 | 0.00 | 0.28 |
|
| iniCall-CNVDetectionResult-method | 0.29 | 0.02 | 0.32 |
|
| iniCall | 0.27 | 0.00 | 0.26 |
|
| integerCopyNumber-CNVDetectionResult-method | 0.3 | 0.0 | 0.3 |
|
| integerCopyNumber | 0.28 | 0.00 | 0.28 |
|
| localAssessments-CNVDetectionResult-method | 0.26 | 0.02 | 0.28 |
|
| localAssessments | 0.39 | 0.00 | 0.39 |
|
| makeRobustCNVR | 0.46 | 0.01 | 0.47 |
|
| normalizeChromosomes | 0.29 | 0.00 | 0.30 |
|
| normalizeGenome | 0.27 | 0.03 | 0.30 |
|
| normalizedData-CNVDetectionResult-method | 0.44 | 0.00 | 0.43 |
|
| normalizedData | 0.29 | 0.00 | 0.30 |
|
| params-CNVDetectionResult-method | 0.27 | 0.00 | 0.27 |
|
| params | 0.30 | 0.00 | 0.29 |
|
| posteriorProbs-CNVDetectionResult-method | 0.25 | 0.00 | 0.25 |
|
| posteriorProbs | 0.26 | 0.00 | 0.27 |
|
| referencecn.mops | 15.99 | 0.03 | 26.22 |
|
| sampleNames-CNVDetectionResult-method | 0.29 | 0.02 | 0.31 |
|
| sampleNames | 0.27 | 0.00 | 0.26 |
|
| segment | 0.03 | 0.00 | 0.04 |
|
| segmentation-CNVDetectionResult-method | 0.28 | 0.02 | 0.29 |
|
| segmentation | 0.3 | 0.0 | 0.3 |
|
| segplot-CNVDetectionResult-method | 1.22 | 0.00 | 1.22 |
|
| segplot | 1.57 | 0.00 | 1.58 |
|
| singlecn.mops | 1.10 | 0.00 | 1.09 |
|