PAPi 1.4.0
Raphael Aggio
| Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/PAPi | | Last Changed Rev: 88838 / Revision: 95116 | | Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ WARNINGS ] | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | WARNINGS | OK |
| morelia | 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 PAPi.buildbin-libdir && mkdir PAPi.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PAPi.buildbin-libdir PAPi_1.4.0.tar.gz >PAPi-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=PAPi.buildbin-libdir --install="check:PAPi-install.out" --force-multiarch --no-vignettes --timings PAPi_1.4.0.tar.gz
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* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/PAPi.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PAPi/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PAPi' version '1.4.0'
* 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 whether package 'PAPi' 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 ... OK
* 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 'papiHtest':
papiHtest
Code: function(inputData, signif.level = 0.05, log.transform = TRUE,
save = TRUE, folder, StatTest, output, adjust.pValue =
TRUE, method = "bonferroni")
Docs: function(inputData, signif.level = 0.05, log.transform = FALSE,
save = TRUE, folder, StatTest, output, adjust.pValue =
TRUE, method = "bonferroni")
Mismatches in argument default values:
Name: 'log.transform' Code: TRUE Docs: FALSE
Codoc mismatches from documentation object 'papiLine':
papiLine
Code: function(inputData, relative = TRUE, save = FALSE, folder,
output = "papi_graph", setRef.cond = FALSE, Ref.cond,
color = "auto", cex.xlab, cex.ylab = 1, position.ylab,
margins = c(25, 8, 2, 2), yscale, dot.size = 1.5,
legend.position, cex.legend = 1, graphWidth = 3000,
graphHeight = 2000, graph.bg = "transparent",
graph.res = 300)
Docs: function(inputData, relative = TRUE, save = TRUE, folder,
output = "papi_graph", setRef.cond = FALSE, Ref.cond,
color = "auto", cex.xlab, cex.ylab = 1, position.ylab,
margins = c(25, 8, 2, 2), yscale, dot.size = 1.5,
legend.position, cex.legend = 1, graphWidth = 3000,
graphHeight = 2000, graph.bg = "transparent",
graph.res = 300)
Mismatches in argument default values:
Name: 'save' Code: FALSE Docs: TRUE
* 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' ... [4s] OK
** running examples for arch 'x64' ... [4s] 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
WARNING: There was 1 warning.
See
'E:/biocbld/bbs-2.14-bioc/meat/PAPi.Rcheck/00check.log'
for details.