BLMA 1.0.0
Tin Nguyen
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/BLMA | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### rm -rf BLMA.buildbin-libdir BLMA.Rcheck && mkdir BLMA.buildbin-libdir BLMA.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BLMA.buildbin-libdir BLMA_1.0.0.tar.gz >BLMA.Rcheck\00install.out 2>&1 && cp BLMA.Rcheck\00install.out BLMA-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=BLMA.buildbin-libdir --install="check:BLMA-install.out" --force-multiarch --no-vignettes --timings BLMA_1.0.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/BLMA.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BLMA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BLMA' version '1.0.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'ROntoTools' 'GSA' 'PADOG' 'limma' 'graph' 'parallel' 'Biobase'
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 'BLMA' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addCLT: warning in pnorm(mean(x), 1/2, sqrt(1/(12 * n)), lower = TRUE):
partial argument match of 'lower' to 'lower.tail'
additiveMethod: warning in pnorm(sum(x), n/2, sqrt(n/12), lower =
TRUE): partial argument match of 'lower' to 'lower.tail'
bilevelAnalysisGeneset : <anonymous>: warning in topTable(fit2, adjust
= "none", sort.by = "logFC", number = nrow(d) * percent, p.value =
pCutoff): partial argument match of 'adjust' to 'adjust.method'
bilevelAnalysisPathway : <anonymous>: warning in topTable(fit2, adjust
= "none", sort.by = "logFC", number = nrow(d) * percent, p.value =
pCutoff): partial argument match of 'adjust' to 'adjust.method'
fisherMethod: warning in pchisq(-2 * sum(log(x)), df = 2 * length(x),
lower = FALSE): partial argument match of 'lower' to 'lower.tail'
intraAnalysisGene : <anonymous>: warning in topTable(fit2, adjust =
"none", sort.by = "none", number = Inf): partial argument match of
'adjust' to 'adjust.method'
intraAnalysisGene: warning in topTable(fit2, adjust = "none", sort.by =
"none", number = Inf): partial argument match of 'adjust' to
'adjust.method'
bilevelAnalysisPathway : <anonymous>: no visible global function
definition for 'Summary'
intraAnalysisGene: no visible binding for global variable 'd'
Undefined global functions or variables:
Summary d
Consider adding
importFrom("methods", "Summary")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 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' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
bilevelAnalysisGeneset 177.63 0.47 178.09
bilevelAnalysisPathway 96.81 0.53 97.35
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
bilevelAnalysisGeneset 149.79 3.28 153.09
bilevelAnalysisPathway 90.10 0.44 90.54
bilevelAnalysisGene 5.04 0.08 5.11
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
Running 'runTests.R'
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 NOTEs
See
'C:/Users/biocbuild/bbs-3.5-bioc/meat/BLMA.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'BLMA' ...
** 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 'BLMA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BLMA' as BLMA_1.0.0.zip
* DONE (BLMA)