BioC 3.3: CHECK report for TransView on morelia
This page was generated on 2015-10-22 17:53:29 -0400 (Thu, 22 Oct 2015).
TransView 1.15.0
Julius Muller
| Snapshot Date: 2015-10-21 20:20:05 -0400 (Wed, 21 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TransView | | 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 | |
Summary
| Package: TransView |
| Version: 1.15.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TransView_1.15.0.tar.gz |
| StartedAt: 2015-10-22 12:12:09 -0400 (Thu, 22 Oct 2015) |
| EndedAt: 2015-10-22 12:14:07 -0400 (Thu, 22 Oct 2015) |
| EllapsedTime: 117.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TransView.Rcheck |
| Warnings: 0 |
Command output
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TransView_1.15.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/TransView.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 ‘TransView/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TransView’ version ‘1.15.0’
* 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 ‘TransView’ can be installed ... [11s/11s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 ... 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 ... NOTE
'library' or 'require' call to ‘RUnit’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in 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 ... NOTE
.slice1T: no visible global function definition for ‘values’
.sliceNT: no visible global function definition for ‘values’
.test: no visible global function definition for ‘defineTestSuite’
.test: no visible global function definition for ‘runTestSuite’
.test: no visible global function definition for ‘printTextProtocol’
annotatePeaks: no visible global function definition for ‘values’
annotatePeaks: no visible global function definition for ‘width’
annotatePeaks: no visible global function definition for ‘mcols’
annotatePeaks: no visible global function definition for ‘strand’
annotatePeaks: no visible global function definition for ‘end<-’
annotatePeaks: no visible global function definition for ‘start<-’
annotatePeaks: no visible global function definition for ‘subjectHits’
annotatePeaks: no visible global function definition for ‘queryHits’
annotatePeaks: no visible global function definition for ‘mid’
annotatePeaks: no visible global function definition for ‘ranges’
annotatePeaks: no visible global function definition for
‘elementLengths’
meltPeak: no visible global function definition for ‘mcols’
meltPeak: no visible global function definition for ‘width’
peak2tss: no visible global function definition for ‘values’
plotTV: no visible global function definition for ‘mcols’
slice1T,DensityContainer-character: no visible global function
definition for ‘values’
sliceNT,DensityContainer-character: no visible global function
definition for ‘values’
Undefined global functions or variables:
defineTestSuite elementLengths end<- mcols mid printTextProtocol
queryHits ranges runTestSuite start<- strand subjectHits values width
* 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [10s/11s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘TransView_unit_tests.R’ [10s/10s]
[10s/10s] 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.3-bioc/meat/TransView.Rcheck/00check.log’
for details.
TransView.Rcheck/00install.out:
* installing *source* package ‘TransView’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rsamtools/include" -fPIC -Wall -mtune=core2 -g -O2 -c R_init_TransView.c -o R_init_TransView.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rsamtools/include" -fPIC -Wall -mtune=core2 -g -O2 -c bin_density.c -o bin_density.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rsamtools/include" -fPIC -Wall -mtune=core2 -g -O2 -c construct_dc.c -o construct_dc.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rsamtools/include" -fPIC -Wall -mtune=core2 -g -O2 -c parse_sam.c -o parse_sam.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rsamtools/include" -fPIC -Wall -mtune=core2 -g -O2 -c slice_dc.c -o slice_dc.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rsamtools/include" -fPIC -Wall -mtune=core2 -g -O2 -c visuals.c -o visuals.o
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 TransView.so R_init_TransView.o bin_density.o construct_dc.o parse_sam.o slice_dc.o visuals.o /Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rsamtools/usrlib//libbam.a /Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rsamtools/usrlib//libbcf.a /Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rsamtools/usrlib//libtabix.a -lz -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
clang: warning: argument unused during compilation: '-pthread'
installing to /Users/biocbuild/bbs-3.3-bioc/meat/TransView.Rcheck/TransView/libs
** R
** inst
** preparing package for lazy loading
No methods found in "IRanges" for requests: mcols
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "IRanges" for requests: mcols
* DONE (TransView)
TransView.Rcheck/TransView-Ex.timings:
| name | user | system | elapsed
|
| DensityContainer-class | 0.003 | 0.000 | 0.004 |
|
| TVResults-class | 0.001 | 0.000 | 0.001 |
|
| TransView-package | 0.000 | 0.000 | 0.001 |
|
| annotatePeaks | 1.850 | 0.013 | 1.933 |
|
| gtf2gr | 0.050 | 0.000 | 0.051 |
|
| macs2gr | 0.041 | 0.001 | 0.042 |
|
| meltPeak | 1.118 | 0.196 | 1.315 |
|
| parseReads | 0.200 | 0.097 | 0.297 |
|
| peak2tss | 0.721 | 0.007 | 0.728 |
|
| plotTV | 0.416 | 0.167 | 0.584 |
|
| plotTVData | 0.299 | 0.182 | 0.481 |
|
| rmTV | 0.332 | 0.117 | 0.449 |
|
| slice1 | 0.156 | 0.177 | 0.333 |
|
| slice1T | 0.575 | 0.032 | 0.659 |
|