cn.mops 1.17.0
Guenter Klambauer
| Snapshot Date: 2015-10-21 20:20:05 -0400 (Wed, 21 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/cn.mops | | Last Changed Rev: 109592 / Revision: 109826 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 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 | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cn.mops_1.17.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/cn.mops.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘cn.mops’ can be installed ... [8s/9s] 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
* 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [51s/90s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
referencecn.mops 9.346 0.026 18.296
cn.mops 8.336 0.138 20.223
calcFractionalCopyNumbers-CNVDetectionResult-method 6.671 0.051 6.723
calcFractionalCopyNumbers 6.421 0.020 6.441
haplocn.mops 1.370 0.015 10.745
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.3-bioc/meat/cn.mops.Rcheck/00check.log’
for details.
* installing *source* package ‘cn.mops’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c R_init_cnmops.c -o R_init_cnmops.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c cnmops.cpp -o cnmops.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c segment.cpp -o segment.o
segment.cpp:64:9: warning: unused variable 'Rf_beta' [-Wunused-variable]
double beta,nn;
^
/Library/Frameworks/R.framework/Resources/include/Rmath.h:217:15: note: expanded from macro 'beta'
#define beta Rf_beta
^
1 warning generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o cn.mops.so R_init_cnmops.o cnmops.o segment.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.3-bioc/meat/cn.mops.Rcheck/cn.mops/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (cn.mops)