oligo 1.34.2
Benilton Carvalho
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/oligo | | Last Changed Rev: 112285 / Revision: 116712 | | Last Changed Date: 2016-01-07 12:33:50 -0800 (Thu, 07 Jan 2016) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | OK | OK | WARNINGS | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ WARNINGS ] | 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 oligo_1.34.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/oligo.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘oligo/DESCRIPTION’ ... OK
* this is package ‘oligo’ version ‘1.34.2’
* 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 ‘oligo’ can be installed ... [16s/18s] OK
* checking installed package size ... NOTE
installed size is 29.3Mb
sub-directories of 1Mb or more:
doc 12.9Mb
scripts 15.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘biomaRt’ ‘AnnotationDbi’ ‘GenomeGraphs’ ‘RCurl’ ‘ff’
A package should be listed in only one of these fields.
* 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 dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘Biobase:::annotatedDataFrameFromMatrix’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function calls to a different package:
.Call("ReadHeader", ..., PACKAGE = "affyio")
.Call("read_abatch", ..., PACKAGE = "affyio")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
image,FeatureSet : .local: warning in matrix(NA, nr = geom[1], nc =
geom[2]): partial argument match of 'nr' to 'nrow'
image,FeatureSet : .local: warning in matrix(NA, nr = geom[1], nc =
geom[2]): partial argument match of 'nc' to 'ncol'
backgroundCorrect,matrix : .local: no visible binding for global
variable ‘intensities’
pmindex,GenericPDInfo : .local: no visible binding for global variable
‘man_fsetid’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'boxplot':
\S4method{boxplot}{FeatureSet}
Code: function(x, which = c("pm", "mm", "bg", "both", "all"), transfo
= log2, nsample = 10000, target = "mps1", ...)
Docs: function(x, which = c("pm", "mm", "bg", "both", "all"), transfo
= log2, nsample = 10000, ...)
Argument names in code not in docs:
target
Mismatches in argument names:
Position: 5 Code: target Docs: ...
Codoc mismatches from documentation object 'hist':
\S4method{hist}{FeatureSet}
Code: function(x, transfo = log2, which = c("pm", "mm", "bg", "both",
"all"), nsample = 10000, target = "mps1", ...)
Docs: function(x, transfo = log2, which = c("pm", "mm", "bg", "both",
"all"), nsample = 10000, ...)
Argument names in code not in docs:
target
Mismatches in argument names:
Position: 5 Code: target Docs: ...
* 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 ... [59s/72s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
preprocessTools 18.807 0.846 19.675
getProbeInfo 12.977 0.679 25.050
read.celfiles 5.106 0.285 5.579
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘doRUnit.R’ [125s/169s]
[125s/169s] 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: 1 WARNING, 5 NOTEs
See
‘/Users/biocbuild/bbs-3.2-bioc/meat/oligo.Rcheck/00check.log’
for details.
* installing *source* package ‘oligo’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include" -fPIC -Wall -mtune=core2 -g -O2 -c DABG.c -o DABG.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include" -fPIC -Wall -mtune=core2 -g -O2 -c ParserGzXYS.c -o ParserGzXYS.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include" -fPIC -Wall -mtune=core2 -g -O2 -c ParserXYS.c -o ParserXYS.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include" -fPIC -Wall -mtune=core2 -g -O2 -c baseProfile.c -o baseProfile.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include" -fPIC -Wall -mtune=core2 -g -O2 -c basecontent.c -o basecontent.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include" -fPIC -Wall -mtune=core2 -g -O2 -c chipbackground.c -o chipbackground.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include" -fPIC -Wall -mtune=core2 -g -O2 -c mas5calls.c -o mas5calls.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include" -fPIC -Wall -mtune=core2 -g -O2 -c rma2.c -o rma2.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include" -fPIC -Wall -mtune=core2 -g -O2 -c rma_common.c -o rma_common.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/preprocessCore/include" -fPIC -Wall -mtune=core2 -g -O2 -c trimmed.c -o trimmed.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 oligo.so DABG.o ParserGzXYS.o ParserXYS.o baseProfile.o basecontent.o chipbackground.o mas5calls.o rma2.o rma_common.o trimmed.o -lz -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/oligo.Rcheck/oligo/libs
** R
** inst
** preparing package for lazy loading
Note: in method for ‘pm<-’ with signature
‘object="TilingFeatureSet",subset="ANY",target="ANY",value="array"’:
expanding the signature to include omitted arguments in definition: =
"missing"
Note: in method for ‘mm<-’ with signature
‘object="TilingFeatureSet",subset="ANY",target="ANY",value="array"’:
expanding the signature to include omitted arguments in definition: =
"missing"
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (oligo)