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### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:seq2pathway.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings seq2pathway_1.39.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/seq2pathway.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘seq2pathway/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘seq2pathway’ version ‘1.39.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘seq2pathway’ can be installed ... WARNING
Found the following significant warnings:
  Warning: program compiled against libxml 212 using older 211
  Warning: replacing previous import ‘WGCNA::cor’ by ‘stats::cor’ when loading ‘seq2pathway’
See ‘/home/biocbuild/bbs-3.21-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 code 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 ... NOTE
Warning: program compiled against libxml 212 using older 211

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... WARNING
Warning: program compiled against libxml 212 using older 211
'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 ... WARNING
Warning: program compiled against libxml 212 using older 211
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Warning: program compiled against libxml 212 using older 211
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Warning: program compiled against libxml 212 using older 211
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
Warning: program compiled against libxml 212 using older 211
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 ... NOTE
checkRd: (-1) runseq2gene.Rd:22-24: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) runseq2gene.Rd:25-27: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) runseq2gene.Rd:28-30: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) runseq2gene.Rd:31-34: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) runseq2gene.Rd:35-37: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) runseq2gene.Rd:41-43: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) runseq2gene.Rd:44-46: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) runseq2gene.Rd:47-49: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) runseq2gene.Rd:50-52: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) runseq2gene.Rd:112-114: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) runseq2gene.Rd:115-117: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) runseq2gene.Rd:118-120: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) runseq2gene.Rd:121-123: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) runseq2gene.Rd:124-127: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) runseq2gene.Rd:128-131: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) runseq2gene.Rd:132-134: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) runseq2gene.Rd:135-137: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) runseq2gene.Rd:138-140: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) runseq2pathway.Rd:26-28: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) runseq2pathway.Rd:29-31: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) runseq2pathway.Rd:32-34: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) runseq2pathway.Rd:35-37: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) runseq2pathway.Rd:38-40: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) runseq2pathway.Rd:44-46: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) runseq2pathway.Rd:47-49: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) runseq2pathway.Rd:50-52: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) runseq2pathway.Rd:53-55: Lost braces in \enumerate; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Warning: program compiled against libxml 212 using older 211
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
* checking Rd \usage sections ... NOTE
Warning: program compiled against libxml 212 using older 211
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
runseq2pathway 40.716  1.205  42.003
runseq2gene    40.117  0.962  41.295
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 6 WARNINGs, 7 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/seq2pathway.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL seq2pathway
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘seq2pathway’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: program compiled against libxml 212 using older 211
Warning: replacing previous import ‘WGCNA::cor’ by ‘stats::cor’ when loading ‘seq2pathway’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: program compiled against libxml 212 using older 211
Warning: replacing previous import ‘WGCNA::cor’ by ‘stats::cor’ when loading ‘seq2pathway’
** testing if installed package can be loaded from final location
Warning: program compiled against libxml 212 using older 211
Warning: replacing previous import ‘WGCNA::cor’ by ‘stats::cor’ when loading ‘seq2pathway’
** testing if installed package keeps a record of temporary installation path
* DONE (seq2pathway)