FEM 1.0.0
Andrew E. Teschendorff , Yinming Jiao
| 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/FEM | | 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 | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK |
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### Running command:
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### rm -rf FEM.buildbin-libdir FEM.Rcheck && mkdir FEM.buildbin-libdir FEM.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=FEM.buildbin-libdir FEM_1.0.0.tar.gz >FEM.Rcheck\00install.out 2>&1 && cp FEM.Rcheck\00install.out FEM-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=FEM.buildbin-libdir --install="check:FEM-install.out" --force-multiarch --no-vignettes --timings FEM_1.0.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/FEM.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'FEM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'FEM' version '1.0.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'Matrix' 'igraph' 'marray' 'corrplot' 'impute' 'limma' 'org.Hs.eg.db'
'graph' 'BiocGenerics'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
vignettes/.IntroDoFEM.Rnw.swm
vignettes/.IntroDoFEM.Rnw.swn
vignettes/.IntroDoFEM.Rnw.swo
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'FEM' 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 ... OK
** 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 ... 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' calls to packages already attached by Depends:
'igraph' 'limma'
Please remove these calls from your code.
Packages in Depends field not imported from:
'BiocGenerics' 'graph'
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
DoEpiMod: no visible binding for global variable 'Entrez.GeneSybo.list'
DoEpiMod: no visible binding for global variable 'toydata'
DoExpMod: no visible binding for global variable 'Entrez.GeneSybo.list'
DoExpMod: no visible binding for global variable 'toydata'
DoFEMbi: no visible binding for global variable 'Entrez.GeneSybo.list'
DoFEMbi: no visible binding for global variable 'toydata'
DoIntEpi450k: no visible binding for global variable 'map450kEID.v'
DoIntEpi450k: no visible binding for global variable 'probeInfoALL.lv'
DoIntFEM450k: no visible binding for global variable 'map450kEID.v'
DoIntFEM450k: no visible binding for global variable 'probeInfoALL.lv'
DoIntFEM450k: no visible binding for global variable
'Entrez.GeneSybo.list'
* checking Rd files ... NOTE
prepare_Rd: DoEpiMod.Rd:53-55: Dropping empty section \details
prepare_Rd: DoEpiMod.Rd:56-62: Dropping empty section \value
prepare_Rd: DoEpiMod.Rd:69-71: Dropping empty section \note
prepare_Rd: DoEpiMod.Rd:66-68: Dropping empty section \author
prepare_Rd: DoEpiMod.Rd:63-65: Dropping empty section \references
prepare_Rd: DoEpiMod.Rd:75-77: Dropping empty section \seealso
prepare_Rd: DoExpMod.Rd:78: Dropping empty section \keyword
prepare_Rd: DoExpMod.Rd:79: Dropping empty section \keyword
prepare_Rd: DoExpMod.Rd:51-53: Dropping empty section \details
prepare_Rd: DoExpMod.Rd:54-60: Dropping empty section \value
prepare_Rd: DoExpMod.Rd:67-69: Dropping empty section \note
prepare_Rd: DoExpMod.Rd:64-66: Dropping empty section \author
prepare_Rd: DoExpMod.Rd:61-63: Dropping empty section \references
prepare_Rd: DoExpMod.Rd:73-75: Dropping empty section \seealso
prepare_Rd: DoExpMod.Rd:76-77: Dropping empty section \examples
prepare_Rd: DoFEMbi.Rd:54-56: Dropping empty section \details
prepare_Rd: DoFEMbi.Rd:57-63: Dropping empty section \value
prepare_Rd: DoFEMbi.Rd:70-72: Dropping empty section \note
prepare_Rd: DoFEMbi.Rd:67-69: Dropping empty section \author
prepare_Rd: DoFEMbi.Rd:64-66: Dropping empty section \references
prepare_Rd: DoFEMbi.Rd:76-78: Dropping empty section \seealso
prepare_Rd: DoIntEpi450k.Rd:34-36: Dropping empty section \details
prepare_Rd: DoIntEpi450k.Rd:37-43: Dropping empty section \value
prepare_Rd: DoIntEpi450k.Rd:50-52: Dropping empty section \note
prepare_Rd: DoIntEpi450k.Rd:47-49: Dropping empty section \author
prepare_Rd: DoIntEpi450k.Rd:44-46: Dropping empty section \references
prepare_Rd: DoIntEpi450k.Rd:56-58: Dropping empty section \seealso
prepare_Rd: DoIntExp.Rd:33-35: Dropping empty section \details
prepare_Rd: DoIntExp.Rd:36-42: Dropping empty section \value
prepare_Rd: DoIntExp.Rd:49-51: Dropping empty section \note
prepare_Rd: DoIntExp.Rd:46-48: Dropping empty section \author
prepare_Rd: DoIntExp.Rd:43-45: Dropping empty section \references
prepare_Rd: DoIntExp.Rd:55-57: Dropping empty section \seealso
prepare_Rd: DoIntExp.Rd:58-59: Dropping empty section \examples
prepare_Rd: DoIntFEM450k.Rd:38-40: Dropping empty section \details
prepare_Rd: DoIntFEM450k.Rd:41-47: Dropping empty section \value
prepare_Rd: DoIntFEM450k.Rd:54-56: Dropping empty section \note
prepare_Rd: DoIntFEM450k.Rd:51-53: Dropping empty section \author
prepare_Rd: DoIntFEM450k.Rd:48-50: Dropping empty section \references
prepare_Rd: DoIntFEM450k.Rd:60-62: Dropping empty section \seealso
prepare_Rd: DoIntFEM450k.Rd:63-65: Dropping empty section \examples
prepare_Rd: DoLimma.Rd:22-24: Dropping empty section \details
prepare_Rd: DoLimma.Rd:25-31: Dropping empty section \value
prepare_Rd: DoLimma.Rd:38-40: Dropping empty section \note
prepare_Rd: DoLimma.Rd:35-37: Dropping empty section \author
prepare_Rd: DoLimma.Rd:32-34: Dropping empty section \references
prepare_Rd: DoLimma.Rd:44-46: Dropping empty section \seealso
prepare_Rd: Entrez.GeneSybo.list.Rd:116-118: Dropping empty section \details
prepare_Rd: Entrez.GeneSybo.list.Rd:119-121: Dropping empty section \source
prepare_Rd: Entrez.GeneSybo.list.Rd:122-124: Dropping empty section \references
prepare_Rd: FEM-package.Rd:36-37: Dropping empty section \seealso
prepare_Rd: FEM-package.Rd:38-40: Dropping empty section \examples
prepare_Rd: FemModShow.Rd:34-36: Dropping empty section \details
prepare_Rd: FemModShow.Rd:37-43: Dropping empty section \value
prepare_Rd: FemModShow.Rd:50-52: Dropping empty section \note
prepare_Rd: FemModShow.Rd:47-49: Dropping empty section \author
prepare_Rd: FemModShow.Rd:44-46: Dropping empty section \references
prepare_Rd: FemModShow.Rd:56-58: Dropping empty section \seealso
prepare_Rd: fembi.o.Rd:16-18: Dropping empty section \details
prepare_Rd: fembi.o.Rd:19-21: Dropping empty section \source
prepare_Rd: fembi.o.Rd:22-24: Dropping empty section \references
prepare_Rd: map450kEID.v.Rd:11-12: Dropping empty section \format
prepare_Rd: map450kEID.v.Rd:13-15: Dropping empty section \details
prepare_Rd: map450kEID.v.Rd:16-18: Dropping empty section \source
prepare_Rd: map450kEID.v.Rd:19-21: Dropping empty section \references
prepare_Rd: probeInfoALL.lv.Rd:11-12: Dropping empty section \format
prepare_Rd: probeInfoALL.lv.Rd:13-15: Dropping empty section \details
prepare_Rd: probeInfoALL.lv.Rd:16-18: Dropping empty section \source
prepare_Rd: probeInfoALL.lv.Rd:19-21: Dropping empty section \references
prepare_Rd: realdata.Rd:11-12: Dropping empty section \format
prepare_Rd: realdata.Rd:13-15: Dropping empty section \details
prepare_Rd: realdata.Rd:16-18: Dropping empty section \source
prepare_Rd: realdata.Rd:19-21: Dropping empty section \references
prepare_Rd: tennodes.Rd:12-13: Dropping empty section \format
prepare_Rd: tennodes.Rd:14-16: Dropping empty section \details
prepare_Rd: tennodes.Rd:17-19: Dropping empty section \source
prepare_Rd: tennodes.Rd:20-22: Dropping empty section \references
prepare_Rd: toydata.Rd:36-38: Dropping empty section \details
prepare_Rd: toydata.Rd:39-41: Dropping empty section \source
prepare_Rd: toydata.Rd:42-44: Dropping empty section \references
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [24s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
DoFEMbi 5.94 0.01 5.97
** running examples for arch 'x64' ... [28s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
DoFEMbi 7.25 0.02 7.33
FemModShow 4.82 0.29 5.12
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R' [34s]
[35s] OK
** running tests for arch 'x64' ...
Running 'runTests.R' [37s]
[38s] 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
NOTE: There were 5 notes.
See
'D:/biocbld/bbs-3.0-bioc/meat/FEM.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'FEM' ...
** 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 'FEM' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'FEM' as FEM_1.0.0.zip
* DONE (FEM)