TransView 1.10.0
Julius Muller
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/TransView | | Last Changed Rev: 95439 / Revision: 102249 | | Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014) |
| zin1 | Linux (Ubuntu 12.04.4 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 | OK | WARNINGS | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK |
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### Running command:
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### /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings TransView_1.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/TransView.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (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 ‘1.10.0’
* 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 ... [13s/14s] 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 ... 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’
* 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 ... WARNING
Found the following file(s) containing GNU extensions:
src/Makevars
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section ‘Writing portable packages’ in
the ‘Writing R Extensions’ manual.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [15s/15s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘TransView_unit_tests.R’ [15s/15s]
[15s/15s] 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
WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
‘/home/biocbuild/bbs-3.0-bioc/meat/TransView.Rcheck/00check.log’
for details.
* installing *source* package ‘TransView’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c R_init_TransView.c -o R_init_TransView.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c bin_density.c -o bin_density.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c construct_dc.c -o construct_dc.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c parse_sam.c -o parse_sam.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c slice_dc.c -o slice_dc.o
slice_dc.c: In function ‘slice_dc’:
slice_dc.c:184:11: warning: ‘slicep’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c visuals.c -o visuals.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.0-bioc/R/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 /home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/usrlib//libbam.a -lz -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.0-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)