Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:08:46 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for seq2pathway on machv2


To the developers/maintainers of the seq2pathway package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/seq2pathway.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1761/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seq2pathway 1.26.0  (landing page)
Arjun Kinstlick
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/seq2pathway
git_branch: RELEASE_3_14
git_last_commit: 2352a4a
git_last_commit_date: 2021-10-26 12:18:36 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: seq2pathway
Version: 1.26.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:seq2pathway.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings seq2pathway_1.26.0.tar.gz
StartedAt: 2022-04-12 18:25:15 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 18:31:02 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 347.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: seq2pathway.Rcheck
Warnings: 2

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:seq2pathway.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings seq2pathway_1.26.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/seq2pathway.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.26.0’
* 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 for sufficient/correct file permissions ... 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 ‘/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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
runseq2gene    45.461  0.918  46.696
runseq2pathway 45.401  0.841  46.527
* 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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/seq2pathway.Rcheck/00check.log’
for details.



Installation output

seq2pathway.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL seq2pathway
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘seq2pathway’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
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: replacing previous import ‘WGCNA::cor’ by ‘stats::cor’ when loading ‘seq2pathway’
** testing if installed package can be loaded from final location
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)

Tests output


Example timings

seq2pathway.Rcheck/seq2pathway-Ex.timings

nameusersystemelapsed
Chipseq_Peak_demo0.0120.0020.014
FisherTest_GO_BP_MF_CC4.5020.1164.623
FisherTest_MsigDB3.0710.0673.143
GRanges_demo0.0020.0020.003
addDescription2.4310.0693.595
dat_RNA0.0150.0020.015
dat_chip0.0020.0010.003
gene2pathway_test1.4080.0211.432
plotTop104.5280.1154.645
runseq2gene45.461 0.91846.696
runseq2pathway45.401 0.84146.527