BioC 3.2: CHECK report for seq2pathway on oaxaca

Package: seq2pathway

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings seq2pathway_1.2.0.tar.gz

StartedAt: 2016-04-23 04:16:42 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 04:21:49 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 307.0 seconds

RetCode: 0

Status:  OK

CheckDir: seq2pathway.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings seq2pathway_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/seq2pathway.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.2.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘seq2pathway’ can be installed ... [16s/16s] 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 ... [107s/137s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
runseq2gene            45.511  0.942  48.894
runseq2pathway         42.860  0.915  51.440
FisherTest_GO_BP_MF_CC  4.334  0.187   5.212
addDescription          0.750  0.011  19.733
* 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
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/seq2pathway.Rcheck/00check.log’
for details.

* installing *source* package ‘seq2pathway’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (seq2pathway)

name	user	system	elapsed
Chipseq_Peak_demo	0.027	0.004	0.031
FisherTest_GO_BP_MF_CC	4.334	0.187	5.212
FisherTest_MsigDB	2.979	0.133	3.464
GRanges_demo	0.002	0.001	0.003
addDescription	0.750	0.011	19.733
dat_RNA	0.016	0.003	0.019
dat_chip	0.003	0.001	0.004
gene2pathway_test	0.943	0.024	1.064
runseq2gene	45.511	0.942	48.894
runseq2pathway	42.860	0.915	51.440