seq2pathway 1.0.1
Xinan Yang with contribution from Lorenzo Pesce and Ana Marija Sokovic
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/seq2pathway | | Last Changed Rev: 108995 / Revision: 109384 | | Last Changed Date: 2015-09-30 05:54:44 -0700 (Wed, 30 Sep 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings seq2pathway_1.0.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/seq2pathway.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘seq2pathway/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘seq2pathway’ version ‘1.0.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘seq2pathway’ can be installed ... [9s/9s] 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
* 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
FAIME_EmpiricalP: no visible binding for global variable
‘gencode_coding’
FisherTest_GO_BP_MF_CC: no visible binding for global variable
‘GO_GENCODE_df_hg_v20’
FisherTest_GO_BP_MF_CC: no visible binding for global variable
‘GO_GENCODE_df_hg_v19’
FisherTest_GO_BP_MF_CC: no visible binding for global variable
‘GO_GENCODE_df_mm_vM4’
FisherTest_GO_BP_MF_CC: no visible binding for global variable
‘GO_GENCODE_df_mm_vM1’
FisherTest_GO_BP_MF_CC: no visible binding for global variable
‘GO_BP_list’
FisherTest_GO_BP_MF_CC: no visible binding for global variable
‘Des_BP_list’
FisherTest_GO_BP_MF_CC: no visible binding for global variable
‘GO_CC_list’
FisherTest_GO_BP_MF_CC: no visible binding for global variable
‘Des_CC_list’
FisherTest_GO_BP_MF_CC: no visible binding for global variable
‘GO_MF_list’
FisherTest_GO_BP_MF_CC: no visible binding for global variable
‘Des_MF_list’
FisherTest_MsigDB: no visible binding for global variable
‘Msig_GENCODE_df_hg_v20’
FisherTest_MsigDB: no visible binding for global variable
‘Msig_GENCODE_df_hg_v19’
FisherTest_MsigDB: no visible binding for global variable
‘Msig_GENCODE_df_mm_vM4’
FisherTest_MsigDB: no visible binding for global variable
‘Msig_GENCODE_df_mm_vM1’
KSrank_EmpiricalP: no visible binding for global variable
‘gencode_coding’
cumulativerank_EmpiricalP: no visible binding for global variable
‘gencode_coding’
gene2pathway_test: no visible binding for global variable ‘GO_BP_list’
gene2pathway_test: no visible binding for global variable ‘Des_BP_list’
gene2pathway_test: no visible binding for global variable ‘GO_MF_list’
gene2pathway_test: no visible binding for global variable ‘Des_MF_list’
gene2pathway_test: no visible binding for global variable ‘GO_CC_list’
gene2pathway_test: no visible binding for global variable ‘Des_CC_list’
runseq2pathway: no visible binding for global variable ‘GO_BP_list’
runseq2pathway: no visible binding for global variable ‘Des_BP_list’
runseq2pathway: no visible binding for global variable ‘GO_MF_list’
runseq2pathway: no visible binding for global variable ‘Des_MF_list’
runseq2pathway: no visible binding for global variable ‘GO_CC_list’
runseq2pathway: no visible binding for global variable ‘Des_CC_list’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [61s/64s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
runseq2pathway 25.103 0.701 25.813
runseq2gene 24.872 0.602 25.678
* 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: 1 NOTE
See
‘/home/biocbuild/bbs-3.1-bioc/meat/seq2pathway.Rcheck/00check.log’
for details.
* installing *source* package ‘seq2pathway’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (seq2pathway)