BioC 3.2: CHECK report for fCI on moscato1
This page was generated on 2015-08-20 13:24:20 -0700 (Thu, 20 Aug 2015).
fCI 0.99.10
Shaojun Tang
| Snapshot Date: 2015-08-19 16:24:33 -0700 (Wed, 19 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/fCI | | Last Changed Rev: 105070 / Revision: 107602 | | Last Changed Date: 2015-06-17 01:48:14 -0700 (Wed, 17 Jun 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 | |
Summary
| Package: fCI
|
| Version: 0.99.10
|
| Command: rm -rf fCI.buildbin-libdir fCI.Rcheck && mkdir fCI.buildbin-libdir fCI.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=fCI.buildbin-libdir fCI_0.99.10.tar.gz >fCI.Rcheck\00install.out 2>&1 && cp fCI.Rcheck\00install.out fCI-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=fCI.buildbin-libdir --install="check:fCI-install.out" --force-multiarch --no-vignettes --timings fCI_0.99.10.tar.gz
|
| StartedAt: 2015-08-20 04:20:15 -0700 (Thu, 20 Aug 2015)
|
| EndedAt: 2015-08-20 04:21:17 -0700 (Thu, 20 Aug 2015)
|
| EllapsedTime: 62.1 seconds
|
| RetCode: 0
|
| Status: WARNINGS
|
| CheckDir: fCI.Rcheck
|
| Warnings: 2
|
Command output
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###
### Running command:
###
### rm -rf fCI.buildbin-libdir fCI.Rcheck && mkdir fCI.buildbin-libdir fCI.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=fCI.buildbin-libdir fCI_0.99.10.tar.gz >fCI.Rcheck\00install.out 2>&1 && cp fCI.Rcheck\00install.out fCI-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=fCI.buildbin-libdir --install="check:fCI-install.out" --force-multiarch --no-vignettes --timings fCI_0.99.10.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/fCI.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 'fCI/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'fCI' version '0.99.10'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'FNN' 'psych' 'gtools' 'zoo' 'rgl' 'grid' 'VennDiagram'
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 'fCI' can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import by 'gtools::logit' when loading 'fCI'
See 'D:/biocbld/bbs-3.2-bioc/meat/fCI.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 ... NOTE
package 'methods' is used but not declared
* 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 ... WARNING
Undocumented S4 classes:
'NPCI'
Undocumented S4 methods:
generic 'find.fci.targets' and siglist 'NPCI'
generic 'show.targets' and siglist 'NPCI'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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' ... [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
* DONE
Status: 2 WARNINGs, 2 NOTEs
See
'D:/biocbld/bbs-3.2-bioc/meat/fCI.Rcheck/00check.log'
for details.
fCI.Rcheck/00install.out:
install for i386
* installing *source* package 'fCI' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import by 'gtools::logit' when loading 'fCI'
in method for 'initialize' with signature '"NPCI"': no definition for class "NPCI"
in method for 'normalization' with signature '"NPCI"': no definition for class "NPCI"
in method for 'populate' with signature '"NPCI"': no definition for class "NPCI"
in method for 'find.fci.targets' with signature '"NPCI"': no definition for class "NPCI"
in method for 'show.targets' with signature '"NPCI"': no definition for class "NPCI"
in method for 'call.npci' with signature '"NPCI"': no definition for class "NPCI"
in method for 'compute' with signature '"NPCI"': no definition for class "NPCI"
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by 'gtools::logit' when loading 'fCI'
install for x64
* installing *source* package 'fCI' ...
** testing if installed package can be loaded
Warning: replacing previous import by 'gtools::logit' when loading 'fCI'
* MD5 sums
packaged installation of 'fCI' as fCI_0.99.10.zip
* DONE (fCI)
fCI.Rcheck/examples_i386/fCI-Ex.timings:
| name | user | system | elapsed
|
| call.npci | 0 | 0 | 0 |
|
| compute | 0 | 0 | 0 |
|
| deg.pairwise.fold.change | 0 | 0 | 0 |
|
| deg.up.down.info | 0 | 0 | 0 |
|
| deseq.median.ratio.normalization | 0.01 | 0.00 | 0.02 |
|
| divergence.multivariate.distributions | 0 | 0 | 0 |
|
| fCI-class | 0 | 0 | 0 |
|
| fCI.call.by.index | 1.08 | 0.24 | 1.31 |
|
| figures | 0 | 0 | 0 |
|
| find.fci.targets | 0 | 0 | 0 |
|
| find.mid.point | 0.53 | 0.01 | 0.54 |
|
| get.fold.large.step | 0 | 0 | 0 |
|
| get.npci.data | 0 | 0 | 0 |
|
| get.npci.distance.matrix | 0.03 | 0.00 | 0.03 |
|
| get.outline.index | 0.03 | 0.00 | 0.03 |
|
| get.protein.fold.step | 0 | 0 | 0 |
|
| get.rank.combinations | 0 | 0 | 0 |
|
| get.rna.fold.step | 0 | 0 | 0 |
|
| intersect.of.lists | 0 | 0 | 0 |
|
| is.installed | 0.02 | 0.00 | 0.02 |
|
| normalization | 0 | 0 | 0 |
|
| npci.gene.by.pvalues | 0.01 | 0.00 | 0.02 |
|
| npci.index.reconsidered | 0.07 | 0.00 | 0.06 |
|
| npci.index.to.be.removed | 0 | 0 | 0 |
|
| npci.venn.diagram | 0.43 | 0.00 | 0.58 |
|
| pairwise.change.occupancy | 0 | 0 | 0 |
|
| populate | 0 | 0 | 0 |
|
| report.target.summary | 0 | 0 | 0 |
|
| show.targets | 0 | 0 | 0 |
|
| summarize | 0.01 | 0.00 | 0.02 |
|
| total.library.size.normalization | 0 | 0 | 0 |
|
| trim.size.normalization | 0.02 | 0.00 | 0.01 |
|
| two.sample.log.ratio | 0 | 0 | 0 |
|
| two.sample.permutation.test | 0.05 | 0.00 | 0.05 |
|
| venndiagram | 0 | 0 | 0 |
|
fCI.Rcheck/examples_x64/fCI-Ex.timings:
| name | user | system | elapsed
|
| call.npci | 0 | 0 | 0 |
|
| compute | 0 | 0 | 0 |
|
| deg.pairwise.fold.change | 0 | 0 | 0 |
|
| deg.up.down.info | 0 | 0 | 0 |
|
| deseq.median.ratio.normalization | 0 | 0 | 0 |
|
| divergence.multivariate.distributions | 0.02 | 0.00 | 0.01 |
|
| fCI-class | 0 | 0 | 0 |
|
| fCI.call.by.index | 0.97 | 0.18 | 1.16 |
|
| figures | 0 | 0 | 0 |
|
| find.fci.targets | 0 | 0 | 0 |
|
| find.mid.point | 0.64 | 0.00 | 0.64 |
|
| get.fold.large.step | 0 | 0 | 0 |
|
| get.npci.data | 0 | 0 | 0 |
|
| get.npci.distance.matrix | 0.03 | 0.00 | 0.03 |
|
| get.outline.index | 0.02 | 0.00 | 0.02 |
|
| get.protein.fold.step | 0 | 0 | 0 |
|
| get.rank.combinations | 0 | 0 | 0 |
|
| get.rna.fold.step | 0 | 0 | 0 |
|
| intersect.of.lists | 0 | 0 | 0 |
|
| is.installed | 0.01 | 0.00 | 0.02 |
|
| normalization | 0 | 0 | 0 |
|
| npci.gene.by.pvalues | 0.02 | 0.00 | 0.02 |
|
| npci.index.reconsidered | 0.09 | 0.00 | 0.09 |
|
| npci.index.to.be.removed | 0 | 0 | 0 |
|
| npci.venn.diagram | 0.64 | 0.01 | 0.72 |
|
| pairwise.change.occupancy | 0 | 0 | 0 |
|
| populate | 0 | 0 | 0 |
|
| report.target.summary | 0 | 0 | 0 |
|
| show.targets | 0 | 0 | 0 |
|
| summarize | 0 | 0 | 0 |
|
| total.library.size.normalization | 0.01 | 0.00 | 0.02 |
|
| trim.size.normalization | 0 | 0 | 0 |
|
| two.sample.log.ratio | 0 | 0 | 0 |
|
| two.sample.permutation.test | 0.08 | 0.00 | 0.08 |
|
| venndiagram | 0 | 0 | 0 |
|