FEM 2.5.1
Andrew E. Teschendorff
| Snapshot Date: 2015-08-19 16:24:33 -0700 (Wed, 19 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/FEM | | Last Changed Rev: 107195 / Revision: 107602 | | Last Changed Date: 2015-08-06 08:01:44 -0700 (Thu, 06 Aug 2015) |
| zin1 | Linux (Ubuntu 14.04.2 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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### rm -rf FEM.buildbin-libdir FEM.Rcheck && mkdir FEM.buildbin-libdir FEM.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=FEM.buildbin-libdir FEM_2.5.1.tar.gz >FEM.Rcheck\00install.out 2>&1 && cp FEM.Rcheck\00install.out FEM-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=FEM.buildbin-libdir --install="check:FEM-install.out" --force-multiarch --no-vignettes --timings FEM_2.5.1.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/FEM.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-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 '2.5.1'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'AnnotationDbi' 'Matrix' 'marray' 'corrplot' 'igraph' '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 ... OK
* checking for portable file names ... OK
* checking whether package 'FEM' can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import by 'graph::intersection' when loading 'FEM'
Warning: replacing previous import by 'graph::union' when loading 'FEM'
Warning: replacing previous import by 'graph::degree' when loading 'FEM'
Warning: replacing previous import by 'graph::edges' when loading 'FEM'
Warning: replacing previous import by 'BiocGenerics::plotMA' when loading 'FEM'
Warning: replacing previous import by 'BiocGenerics::as.vector' when loading 'FEM'
Warning: replacing previous import by 'BiocGenerics::.__C__dist' when loading 'FEM'
Warning: replacing previous import by 'BiocGenerics::normalize' when loading 'FEM'
See 'D:/biocbld/bbs-3.2-bioc/meat/FEM.Rcheck/00install.out' for details.
* 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 ... OK
* 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 global function definition for 'mappedkeys'
DoExpMod: no visible global function definition for 'mappedkeys'
DoFEMbi: no visible global function definition for 'mappedkeys'
GenStatM: no visible binding for global variable 'probe450kfemanno'
* checking Rd files ... NOTE
prepare_Rd: DoEpiMod.Rd:44-46: Dropping empty section \details
prepare_Rd: DoEpiMod.Rd:71-73: Dropping empty section \note
prepare_Rd: DoEpiMod.Rd:77-79: Dropping empty section \seealso
prepare_Rd: DoExpMod.Rd:93: Dropping empty section \keyword
prepare_Rd: DoExpMod.Rd:94: Dropping empty section \keyword
prepare_Rd: DoExpMod.Rd:46-48: Dropping empty section \details
prepare_Rd: DoExpMod.Rd:72-74: Dropping empty section \note
prepare_Rd: DoExpMod.Rd:78-80: Dropping empty section \seealso
prepare_Rd: DoFEMbi.Rd:45-47: Dropping empty section \details
prepare_Rd: DoFEMbi.Rd:71-73: Dropping empty section \note
prepare_Rd: DoFEMbi.Rd:77-79: Dropping empty section \seealso
prepare_Rd: DoIntEpi450k.Rd:30-32: Dropping empty section \details
prepare_Rd: DoIntEpi450k.Rd:47-49: Dropping empty section \note
prepare_Rd: DoIntEpi450k.Rd:53-55: Dropping empty section \seealso
prepare_Rd: DoIntEpi450k.Rd:56-58: Dropping empty section \examples
prepare_Rd: DoIntExp.Rd:29-31: Dropping empty section \details
prepare_Rd: DoIntExp.Rd:47-49: Dropping empty section \note
prepare_Rd: DoIntExp.Rd:53-55: Dropping empty section \seealso
prepare_Rd: DoIntExp.Rd:56-57: Dropping empty section \examples
prepare_Rd: DoIntFEM450k.Rd:41-43: Dropping empty section \details
prepare_Rd: DoIntFEM450k.Rd:60-62: Dropping empty section \note
prepare_Rd: DoIntFEM450k.Rd:66-68: Dropping empty section \seealso
prepare_Rd: DoIntFEM450k.Rd:69-71: Dropping empty section \examples
prepare_Rd: FEM-package.Rd:47-48: Dropping empty section \seealso
prepare_Rd: FEM-package.Rd:49-51: Dropping empty section \examples
prepare_Rd: FemModShow.Rd:33-35: Dropping empty section \details
prepare_Rd: FemModShow.Rd:47-49: Dropping empty section \note
prepare_Rd: FemModShow.Rd:53-55: Dropping empty section \seealso
prepare_Rd: GenStatM.Rd:25-27: Dropping empty section \details
prepare_Rd: GenStatM.Rd:43-45: Dropping empty section \note
prepare_Rd: GenStatM.Rd:49-51: Dropping empty section \seealso
prepare_Rd: GenStatM.Rd:52-54: Dropping empty section \examples
prepare_Rd: GenStatR.Rd:26-28: Dropping empty section \details
prepare_Rd: GenStatR.Rd:43-45: Dropping empty section \note
prepare_Rd: GenStatR.Rd:49-51: Dropping empty section \seealso
prepare_Rd: GenStatR.Rd:52-54: Dropping empty section \examples
prepare_Rd: Realdata.Rd:28-29: Dropping empty section \format
prepare_Rd: Realdata.Rd:30-32: Dropping empty section \details
prepare_Rd: Realdata.Rd:33-35: Dropping empty section \source
prepare_Rd: Toydata.Rd:27-29: Dropping empty section \details
prepare_Rd: Toydata.Rd:30-32: Dropping empty section \source
prepare_Rd: probe450kfemanno.Rd:27-28: Dropping empty section \format
prepare_Rd: probe450kfemanno.Rd:29-30: Dropping empty section \details
prepare_Rd: probe450kfemanno.Rd:31-33: Dropping empty section \source
prepare_Rd: probe450kfemanno.Rd:40-41: Dropping empty section \examples
* 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 ... WARNING
Warning: package needs dependence on R (>= 2.10)
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... NOTE
The following files contain a license that requires
distribution of original sources:
'xcolor.sty'
Please ensure that you have complied with it.
* checking examples ...
** running examples for arch 'i386' ... [69s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
FemModShow 13.37 0.67 14.04
DoFEMbi 12.73 0.03 12.76
DoExpMod 12.01 0.01 12.03
DoEpiMod 11.78 0.05 11.92
Toydata 11.64 0.18 11.81
** running examples for arch 'x64' ... [83s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
DoFEMbi 14.95 0.05 14.99
Toydata 14.75 0.17 14.93
FemModShow 13.59 0.67 14.29
DoEpiMod 13.99 0.04 16.88
DoExpMod 14.01 0.01 14.54
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R' [18s]
[19s] OK
** running tests for arch 'x64' ...
Running 'runTests.R' [25s]
[25s] 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: 2 WARNINGs, 4 NOTEs
See
'D:/biocbld/bbs-3.2-bioc/meat/FEM.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'FEM' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import by 'graph::intersection' when loading 'FEM'
Warning: replacing previous import by 'graph::union' when loading 'FEM'
Warning: replacing previous import by 'graph::degree' when loading 'FEM'
Warning: replacing previous import by 'graph::edges' when loading 'FEM'
Warning: replacing previous import by 'BiocGenerics::plotMA' when loading 'FEM'
Warning: replacing previous import by 'BiocGenerics::as.vector' when loading 'FEM'
Warning: replacing previous import by 'BiocGenerics::.__C__dist' when loading 'FEM'
Warning: replacing previous import by 'BiocGenerics::normalize' when loading 'FEM'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by 'graph::intersection' when loading 'FEM'
Warning: replacing previous import by 'graph::union' when loading 'FEM'
Warning: replacing previous import by 'graph::degree' when loading 'FEM'
Warning: replacing previous import by 'graph::edges' when loading 'FEM'
Warning: replacing previous import by 'BiocGenerics::plotMA' when loading 'FEM'
Warning: replacing previous import by 'BiocGenerics::as.vector' when loading 'FEM'
Warning: replacing previous import by 'BiocGenerics::.__C__dist' when loading 'FEM'
Warning: replacing previous import by 'BiocGenerics::normalize' when loading 'FEM'
install for x64
* installing *source* package 'FEM' ...
** testing if installed package can be loaded
Warning: replacing previous import by 'graph::edges' when loading 'FEM'
Warning: replacing previous import by 'graph::intersection' when loading 'FEM'
Warning: replacing previous import by 'graph::degree' when loading 'FEM'
Warning: replacing previous import by 'graph::union' when loading 'FEM'
Warning: replacing previous import by 'BiocGenerics::plotMA' when loading 'FEM'
Warning: replacing previous import by 'BiocGenerics::as.vector' when loading 'FEM'
Warning: replacing previous import by 'BiocGenerics::.__C__dist' when loading 'FEM'
Warning: replacing previous import by 'BiocGenerics::normalize' when loading 'FEM'
* MD5 sums
packaged installation of 'FEM' as FEM_2.5.1.zip
* DONE (FEM)