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### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:seq2pathway.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings seq2pathway_1.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/seq2pathway.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.22.0'
* 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 ... NOTE
Found the following hidden files and directories:
  vignettes/.RData
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* 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'
plotTop10: no visible binding for global variable 'Fisher_odds'
plotTop10: no visible binding for global variable 'FDR'
plotTop10: no visible global function definition for 'barplot'
plotTop10: no visible global function definition for 'lines'
plotTop10: no visible global function definition for 'text'
plotTop10: no visible global function definition for 'abline'
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 FDR Fisher_odds 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 abline barplot data fisher.test gencode_coding
  head ks.test lines p.adjust read.table setTxtProgressBar text
  txtProgressBar write.table
Consider adding
  importFrom("graphics", "abline", "barplot", "lines", "text")
  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 ... WARNING
File 'data/datalist' contains malformed line(s):
  ''
* 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' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
addDescription 11.21   0.03   18.23
runseq2pathway  1.62   0.29   37.53
runseq2gene     0.02   0.00   43.86
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
addDescription 10.39   0.00   17.02
runseq2pathway  1.65   0.18   33.58
runseq2gene     0.02   0.00   28.76
* 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 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/seq2pathway.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/seq2pathway_1.22.0.tar.gz && rm -rf seq2pathway.buildbin-libdir && mkdir seq2pathway.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=seq2pathway.buildbin-libdir seq2pathway_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL seq2pathway_1.22.0.zip && rm seq2pathway_1.22.0.tar.gz seq2pathway_1.22.0.zip
###
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100 1586k  100 1586k    0     0  44.0M      0 --:--:-- --:--:-- --:--:-- 45.5M

install for i386

* installing *source* package 'seq2pathway' ...
** using staged installation
** 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  
    plotTop10                               html  
    runseq2gene                             html  
    runseq2pathway                          html  
** building package indices
** installing vignettes
   'seq2pathwaypackage.Rnw' 
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'seq2pathway' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'seq2pathway' as seq2pathway_1.22.0.zip
* DONE (seq2pathway)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'seq2pathway' successfully unpacked and MD5 sums checked