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BioC 3.6: CHECK report for seq2pathway on malbec1

This page was generated on 2017-08-16 13:22:51 -0400 (Wed, 16 Aug 2017).

Package 1222/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seq2pathway 1.9.0
Xinan Yang with contribution from Lorenzo Pesce and Ana Marija Sokovic
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seq2pathway
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: seq2pathway
Version: 1.9.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings seq2pathway_1.9.0.tar.gz
StartedAt: 2017-08-16 02:20:12 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 02:23:22 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 190.9 seconds
RetCode: 0
Status:  OK 
CheckDir: seq2pathway.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings seq2pathway_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/seq2pathway.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.9.0’
* 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 ... 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 global function definition for ‘data’
FAIME_EmpiricalP: no visible binding for global variable
  ‘gencode_coding’
FisherTest_GO_BP_MF_CC: no visible global function definition for
  ‘data’
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
  ‘GO_MF_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_BP_list’
FisherTest_GO_BP_MF_CC: no visible binding for global variable
  ‘Des_MF_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_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 global function definition for
  ‘fisher.test’
FisherTest_GO_BP_MF_CC: no visible global function definition for
  ‘p.adjust’
FisherTest_MsigDB: no visible global function definition for ‘data’
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’
FisherTest_MsigDB: no visible global function definition for
  ‘fisher.test’
FisherTest_MsigDB: no visible global function definition for ‘p.adjust’
KSrank: no visible global function definition for ‘ks.test’
KSrank_EmpiricalP: no visible global function definition for ‘data’
KSrank_EmpiricalP: no visible binding for global variable
  ‘gencode_coding’
KSrank_EmpiricalP: no visible global function definition for ‘ks.test’
Normalize_F: no visible global function definition for ‘head’
cumulativerank_EmpiricalP: no visible global function definition for
  ‘data’
cumulativerank_EmpiricalP: no visible binding for global variable
  ‘gencode_coding’
gene2pathway_test: no visible global function definition for ‘data’
gene2pathway_test: no visible binding for global variable ‘GO_BP_list’
gene2pathway_test: no visible binding for global variable ‘GO_MF_list’
gene2pathway_test: no visible binding for global variable ‘GO_CC_list’
gene2pathway_test: no visible binding for global variable ‘Des_BP_list’
gene2pathway_test: no visible binding for global variable ‘Des_CC_list’
gene2pathway_test: no visible binding for global variable ‘Des_MF_list’
rungene2pathway_EmpiricalP: no visible global function definition for
  ‘txtProgressBar’
rungene2pathway_EmpiricalP: no visible global function definition for
  ‘setTxtProgressBar’
runseq2gene: no visible global function definition for ‘write.table’
runseq2gene: no visible global function definition for ‘read.table’
runseq2pathway: no visible global function definition for ‘data’
runseq2pathway: no visible binding for global variable ‘GO_BP_list’
runseq2pathway: no visible binding for global variable ‘GO_MF_list’
runseq2pathway: no visible binding for global variable ‘GO_CC_list’
runseq2pathway: no visible binding for global variable ‘Des_BP_list’
runseq2pathway: no visible binding for global variable ‘Des_CC_list’
runseq2pathway: no visible binding for global variable ‘Des_MF_list’
runseq2pathway: no visible global function definition for ‘write.table’
runseq2pathway: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  Des_BP_list Des_CC_list Des_MF_list GO_BP_list GO_CC_list
  GO_GENCODE_df_hg_v19 GO_GENCODE_df_hg_v20 GO_GENCODE_df_mm_vM1
  GO_GENCODE_df_mm_vM4 GO_MF_list Msig_GENCODE_df_hg_v19
  Msig_GENCODE_df_hg_v20 Msig_GENCODE_df_mm_vM1 Msig_GENCODE_df_mm_vM4
  data fisher.test gencode_coding head ks.test p.adjust read.table
  setTxtProgressBar txtProgressBar write.table
Consider adding
  importFrom("stats", "fisher.test", "ks.test", "p.adjust")
  importFrom("utils", "data", "head", "read.table", "setTxtProgressBar",
             "txtProgressBar", "write.table")
to your NAMESPACE file.
* 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 ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
runseq2gene    25.528  0.588  26.741
runseq2pathway 24.356  0.604  24.977
* 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-3.6-bioc/meat/seq2pathway.Rcheck/00check.log’
for details.


seq2pathway.Rcheck/00install.out:

* 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)

seq2pathway.Rcheck/seq2pathway-Ex.timings:

nameusersystemelapsed
Chipseq_Peak_demo0.0040.0000.006
FisherTest_GO_BP_MF_CC3.4360.0123.494
FisherTest_MsigDB1.9600.0041.966
GRanges_demo0.0040.0000.002
addDescription0.3800.0003.591
dat_RNA0.0200.0000.019
dat_chip0.0040.0000.002
gene2pathway_test0.6080.0360.642
runseq2gene25.528 0.58826.741
runseq2pathway24.356 0.60424.977