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### Running command:
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###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:seq2pathway.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings seq2pathway_1.26.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/seq2pathway.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.26.0'
* 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 ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'WGCNA::cor' by 'stats::cor' when loading 'seq2pathway'
See 'C:/Users/biocbuild/bbs-3.14-bioc/meat/seq2pathway.Rcheck/00install.out' for details.
* 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 ... NOTE
Found the following CITATION file in a non-standard place:
  CITATION
Most likely 'inst/CITATION' should be used instead.
* 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 ... WARNING
'library' or 'require' call not declared from: 'biomaRt'
'library' or 'require' call to 'biomaRt' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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_v36'
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_vM25'
FisherTest_GO_BP_MF_CC: no visible binding for global variable
  'GO_GENCODE_df_mm_vM1'
FisherTest_MsigDB: no visible global function definition for 'data'
FisherTest_MsigDB: no visible binding for global variable
  'Msig_GENCODE_df_hg_v36'
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_vM25'
FisherTest_MsigDB: no visible binding for global variable
  'Msig_GENCODE_df_mm_vM1'
KSrank_EmpiricalP: no visible global function definition for 'data'
KSrank_EmpiricalP: no visible binding for global variable
  'gencode_coding'
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_v36
  GO_GENCODE_df_mm_vM1 GO_GENCODE_df_mm_vM25 GO_MF_list
  Msig_GENCODE_df_hg_v19 Msig_GENCODE_df_hg_v36 Msig_GENCODE_df_mm_vM1
  Msig_GENCODE_df_mm_vM25 abline barplot data gencode_coding head lines
  read.table setTxtProgressBar text txtProgressBar write.table
Consider adding
  importFrom("graphics", "abline", "barplot", "lines", "text")
  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 (user + system) or elapsed time > 5s
               user system elapsed
addDescription 4.20   0.03    5.40
runseq2pathway 1.57   0.09   34.39
runseq2gene    0.01   0.00   38.84
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
runseq2pathway 1.28   0.08   30.25
runseq2gene    0.00   0.01   32.61
* 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: 2 WARNINGs, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/seq2pathway.Rcheck/00check.log'
for details.