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CHECK report for seq2pathway on tokay1

This page was generated on 2019-04-13 11:24:51 -0400 (Sat, 13 Apr 2019).

Package 1415/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seq2pathway 1.14.0
Xinan Yang with contribution from Lorenzo Pesce and Ana Marija Sokovic
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/seq2pathway
Branch: RELEASE_3_8
Last Commit: 11464ae
Last Changed Date: 2018-10-30 11:41:56 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: seq2pathway
Version: 1.14.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:seq2pathway.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings seq2pathway_1.14.0.tar.gz
StartedAt: 2019-04-13 05:24:48 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 05:31:37 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 409.4 seconds
RetCode: 0
Status:  OK  
CheckDir: seq2pathway.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:seq2pathway.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings seq2pathway_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/seq2pathway.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'seq2pathway/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'seq2pathway' version '1.14.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 '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
* 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
* 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 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
runseq2pathway 1.78   0.25   38.32
addDescription 0.39   0.01    7.25
runseq2gene    0.01   0.00   34.04
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
runseq2pathway 1.72   0.28   36.89
runseq2gene    0.00   0.00   34.36
* 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
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/seq2pathway.Rcheck/00check.log'
for details.



Installation output

seq2pathway.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/seq2pathway_1.14.0.tar.gz && rm -rf seq2pathway.buildbin-libdir && mkdir seq2pathway.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=seq2pathway.buildbin-libdir seq2pathway_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL seq2pathway_1.14.0.zip && rm seq2pathway_1.14.0.tar.gz seq2pathway_1.14.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1495k  100 1495k    0     0  25.8M      0 --:--:-- --:--:-- --:--:-- 27.5M

install for i386

* installing *source* package 'seq2pathway' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'seq2pathway'
    finding HTML links ... done
    Chipseq_Peak_demo                       html  
    FisherTest_GO_BP_MF_CC                  html  
    FisherTest_MsigDB                       html  
    GRanges_demo                            html  
    addDescription                          html  
    dat_RNA                                 html  
    dat_chip                                html  
    gene2pathway_test                       html  
    runseq2gene                             html  
    runseq2pathway                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'seq2pathway' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'seq2pathway' as seq2pathway_1.14.0.zip
* DONE (seq2pathway)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'seq2pathway' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

seq2pathway.Rcheck/examples_i386/seq2pathway-Ex.timings

nameusersystemelapsed
Chipseq_Peak_demo000
FisherTest_GO_BP_MF_CC3.820.084.09
FisherTest_MsigDB2.230.002.33
GRanges_demo0.020.020.03
addDescription0.390.017.25
dat_RNA0.020.000.01
dat_chip0.000.020.02
gene2pathway_test0.940.371.75
runseq2gene 0.01 0.0034.04
runseq2pathway 1.78 0.2538.32

seq2pathway.Rcheck/examples_x64/seq2pathway-Ex.timings

nameusersystemelapsed
Chipseq_Peak_demo0.060.000.06
FisherTest_GO_BP_MF_CC3.460.063.52
FisherTest_MsigDB1.730.001.74
GRanges_demo000
addDescription0.230.033.25
dat_RNA0.020.000.02
dat_chip000
gene2pathway_test0.830.201.03
runseq2gene 0.00 0.0034.36
runseq2pathway 1.72 0.2836.89