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CHECK report for genArise on malbec2

This page was generated on 2020-10-17 11:54:48 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE genArise PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 671/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genArise 1.64.0
IFC Development Team
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/genArise
Branch: RELEASE_3_11
Last Commit: 5d4235f
Last Changed Date: 2020-04-27 14:10:16 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: genArise
Version: 1.64.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:genArise.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings genArise_1.64.0.tar.gz
StartedAt: 2020-10-17 01:33:58 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 01:34:40 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 42.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: genArise.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:genArise.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings genArise_1.64.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/genArise.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genArise/DESCRIPTION’ ... OK
* this is package ‘genArise’ version ‘1.64.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘genArise’ can be installed ... WARNING
Found the following significant warnings:
  Note: possible error in 'pdf(paste(name, ".pdf", ': unused argument (horiz = FALSE) 
  Note: possible error in 'pdf(paste(name, "OriginalCy3vsCy5.pdf", ': unused argument (horiz = F) 
  Note: possible error in 'pdf(paste(name, "OriginalRvsI.pdf", ': unused argument (horiz = F) 
  Note: possible error in 'pdf(paste(name, "OriginalMvsA.pdf", ': unused argument (horiz = F) 
  Note: possible error in 'pdf(paste(name, "CorrectedCy3vsCy5.pdf", ': unused argument (horiz = F) 
  Note: possible error in 'pdf(paste(name, "CorrectedRvsI.pdf", ': unused argument (horiz = F) 
  Note: possible error in 'pdf(paste(name, "CorrectedMvsA.pdf", ': unused argument (horiz = F) 
  Note: possible error in 'pdf(paste(name, "NormalCy3vsCy5.pdf", ': unused argument (horiz = F) 
  Note: possible error in 'pdf(paste(name, "NormalRvsI.pdf", ': unused argument (horiz = F) 
  Note: possible error in 'pdf(paste(name, "NormalMvsA.pdf", ': unused argument (horiz = F) 
  Note: possible error in 'pdf(paste(name, "FilterCy3vsCy5.pdf", ': unused argument (horiz = F) 
  Note: possible error in 'pdf(paste(name, "FilterRvsI.pdf", ': unused argument (horiz = F) 
  Note: possible error in 'pdf(paste(name, "FilterMvsA.pdf", ': unused argument (horiz = F) 
  Note: possible error in 'pdf(paste(name, "NoDuplicatesCy3vsCy5.pdf", ': unused argument (horiz = F) 
  Note: possible error in 'pdf(paste(name, "NoDuplicatesRvsI.pdf", ': unused argument (horiz = F) 
  Note: possible error in 'pdf(paste(name, "NoDuplicatesMvsA.pdf", ': unused argument (horiz = F) 
  Note: possible error in 'pdf(name, horiz = F, ': unused argument (horiz = F) 
  Note: possible error in 'pdf(paste(name, "R&G.pdf", ': unused argument (horiz = F) 
  Note: possible error in 'pdf(paste(name, "BgCy5.pdf", ': unused argument (horiz = F) 
  Note: possible error in 'pdf(paste(name, "BgCy3.pdf", ': unused argument (horiz = F) 
  Note: possible error in 'pdf(paste(name, "Swap.pdf", ': unused argument (horiz = F) 
See ‘/home/biocbuild/bbs-3.11-bioc/meat/genArise.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
A package should be listed in only one of these fields.
* 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
* 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 ... NOTE
Packages in Depends field not imported from:
  ‘locfit’ ‘tkrplot’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
genMerge: warning in assign(gene.association.file$V1[i], list(GO =
  gene.association.file$V2[i]), env = GMRGgenomehash): partial argument
  match of 'env' to 'envir'
genMerge: warning in assign(des.file$V1[i], list(Description =
  des.file$V2[i]), env = descriptionHash): partial argument match of
  'env' to 'envir'
genMerge: warning in ls(env = GMRGgenomehash): partial argument match
  of 'env' to 'envir'
genMerge: warning in get(population.file$V1[i], env = GMRGgenomehash):
  partial argument match of 'env' to 'envir'
genMerge: warning in assign(unique.list$values[i], list(count =
  unique.list$lengths[i], frequence =
  unique.list$lengths[i]/total.no.detected.genes), env = output.hash):
  partial argument match of 'env' to 'envir'
genMerge: warning in get(study.genes.file$V1[i], env = GMRGgenomehash):
  partial argument match of 'env' to 'envir'
genMerge: warning in get(updownGMRGs[k], env = id.hash): partial
  argument match of 'env' to 'envir'
genMerge: warning in assign(updownGMRGs[k], unique.list, env =
  id.hash): partial argument match of 'env' to 'envir'
genMerge: warning in assign(updownGMRGs[k], study.genes.file$V1[i], env
  = id.hash): partial argument match of 'env' to 'envir'
genMerge: warning in get(output2$uniqueUpDownGMRGIDs[i], env =
  output.hash): partial argument match of 'env' to 'envir'
genMerge: warning in get(output2$uniqueUpDownGMRGIDs[k], env =
  descriptionHash): partial argument match of 'env' to 'envir'
genMerge: warning in get(output2$uniqueUpDownGMRGIDs[k], env =
  id.hash): partial argument match of 'env' to 'envir'
Zscore.points : <anonymous>: no visible global function definition for
  ‘tkrreplot’
Zscore.points : <anonymous>: possible error in pdf(paste(name, ".pdf",
  sep = ""), horiz = FALSE, height = 8, width = 8, title = name):
  unused argument (horiz = FALSE)
Zscore.points: no visible global function definition for ‘tkrplot’
analysis.window : bg.question: no visible binding for '<<-' assignment
  to ‘op.counter’
analysis.window : bg.question: no visible binding for global variable
  ‘op.counter’
analysis.window : normalized.gui: no visible binding for '<<-'
  assignment to ‘op.counter’
analysis.window : normalized.gui: no visible binding for global
  variable ‘op.counter’
analysis.window : normalized.gui: no visible global function definition
  for ‘tkrreplot’
analysis.window : filter.gui: no visible binding for '<<-' assignment
  to ‘op.counter’
analysis.window : filter.gui: no visible binding for global variable
  ‘op.counter’
analysis.window : filter.gui: no visible global function definition for
  ‘tkrreplot’
analysis.window : remove.duplicates.gui: no visible binding for '<<-'
  assignment to ‘op.counter’
analysis.window : remove.duplicates.gui: no visible binding for global
  variable ‘op.counter’
analysis.window : remove.duplicates.gui: no visible global function
  definition for ‘tkrreplot’
analysis.window : <anonymous>: no visible global function definition
  for ‘tkrreplot’
analysis.window : cys.plot: no visible global function definition for
  ‘tkrreplot’
analysis.window : <anonymous>: possible error in pdf(paste(name,
  "OriginalCy3vsCy5.pdf", sep = "_"), horiz = F, height = 8, width = 8,
  title = paste(name, "OriginalCy3vsCy5.pdf", sep = "_")): unused
  argument (horiz = F)
analysis.window : <anonymous>: possible error in pdf(paste(name,
  "OriginalRvsI.pdf", sep = "_"), horiz = F, height = 8, width = 8,
  title = paste(name, "OriginalRvsI.pdf", sep = "_")): unused argument
  (horiz = F)
analysis.window : <anonymous>: possible error in pdf(paste(name,
  "OriginalMvsA.pdf", sep = "_"), horiz = F, height = 8, width = 8,
  title = paste(name, "OriginalMvsA.pdf", sep = "_")): unused argument
  (horiz = F)
analysis.window : <anonymous>: possible error in pdf(paste(name,
  "CorrectedCy3vsCy5.pdf", sep = "_"), horiz = F, height = 8, width =
  8, title = paste(name, "CorrectedCy3vsCy5.pdf", sep = "_")): unused
  argument (horiz = F)
analysis.window : <anonymous>: possible error in pdf(paste(name,
  "CorrectedRvsI.pdf", sep = "_"), horiz = F, height = 8, width = 8,
  title = paste(name, "CorrectedRvsI.pdf", sep = "_")): unused argument
  (horiz = F)
analysis.window : <anonymous>: possible error in pdf(paste(name,
  "CorrectedMvsA.pdf", sep = "_"), horiz = F, height = 8, width = 8,
  title = paste(name, "CorrectedMvsA.pdf", sep = "_")): unused argument
  (horiz = F)
analysis.window : <anonymous>: possible error in pdf(paste(name,
  "NormalCy3vsCy5.pdf", sep = "_"), horiz = F, height = 8, width = 8,
  title = paste(name, "NormalCy3vsCy5.pdf", sep = "_")): unused
  argument (horiz = F)
analysis.window : <anonymous>: possible error in pdf(paste(name,
  "NormalRvsI.pdf", sep = "_"), horiz = F, height = 8, width = 8, title
  = paste(name, "NormalRvsI.pdf", sep = "_")): unused argument (horiz =
  F)
analysis.window : <anonymous>: possible error in pdf(paste(name,
  "NormalMvsA.pdf", sep = "_"), horiz = F, height = 8, width = 8, title
  = paste(name, "NormalMvsA.pdf", sep = "_")): unused argument (horiz =
  F)
analysis.window : <anonymous>: possible error in pdf(paste(name,
  "FilterCy3vsCy5.pdf", sep = "_"), horiz = F, height = 8, width = 8,
  title = paste(name, "FilterCy3vsCy5.pdf", sep = "_")): unused
  argument (horiz = F)
analysis.window : <anonymous>: possible error in pdf(paste(name,
  "FilterRvsI.pdf", sep = "_"), horiz = F, height = 8, width = 8, title
  = paste(name, "FilterRvsI.pdf", sep = "_")): unused argument (horiz =
  F)
analysis.window : <anonymous>: possible error in pdf(paste(name,
  "FilterMvsA.pdf", sep = "_"), horiz = F, height = 8, width = 8, title
  = paste(name, "FilterMvsA.pdf", sep = "_")): unused argument (horiz =
  F)
analysis.window : <anonymous>: possible error in pdf(paste(name,
  "NoDuplicatesCy3vsCy5.pdf", sep = "_"), horiz = F, height = 8, width
  = 8, title = paste(name, "NoDuplicatesCy3vsCy5.pdf", sep = "_")):
  unused argument (horiz = F)
analysis.window : <anonymous>: possible error in pdf(paste(name,
  "NoDuplicatesRvsI.pdf", sep = "_"), horiz = F, height = 8, width = 8,
  title = paste(name, "NoDuplicatesRvsI.pdf", sep = "_")): unused
  argument (horiz = F)
analysis.window : <anonymous>: possible error in pdf(paste(name,
  "NoDuplicatesMvsA.pdf", sep = "_"), horiz = F, height = 8, width = 8,
  title = paste(name, "NoDuplicatesMvsA.pdf", sep = "_")): unused
  argument (horiz = F)
analysis.window: no visible global function definition for ‘tkrplot’
analysis.window: no visible binding for '<<-' assignment to
  ‘op.counter’
analysis.window: no visible binding for global variable ‘op.counter’
annotations: no visible global function definition for ‘print.xtable’
genArise.init: no visible binding for '<<-' assignment to ‘op.counter’
genArise.init : nuevo.project: no visible global function definition
  for ‘select.experiments’
global.norm: no visible global function definition for ‘locfit’
global.norm: no visible global function definition for ‘rbox’
grid.norm: no visible global function definition for ‘locfit’
grid.norm: no visible global function definition for ‘rbox’
old.project : selected.zscore: no visible global function definition
  for ‘tkrreplot’
old.project : save.pdf: possible error in pdf(name, horiz = F, height =
  8, width = 8, title = paste(name, sep = "_")): unused argument (horiz
  = F)
old.project : imageLimma.plot: no visible global function definition
  for ‘tkrreplot’
old.project : otra.funcion: no visible global function definition for
  ‘tkrreplot’
old.project: no visible global function definition for ‘tkrplot’
old.project : <anonymous>: no visible global function definition for
  ‘tkrreplot’
old.project : <anonymous>: possible error in pdf(paste(name, ".pdf",
  sep = ""), horiz = FALSE, height = 8, width = 8, title = name):
  unused argument (horiz = FALSE)
principal : save.as.pdf: possible error in pdf(paste(name, "R&G.pdf",
  sep = "_"), horiz = F, height = 8, width = 8, title = paste(name,
  "R&G.pdf", sep = "_")): unused argument (horiz = F)
principal : save.as.pdf: possible error in pdf(paste(name, "BgCy5.pdf",
  sep = "_"), horiz = F, height = 8, width = 8, title = paste(name,
  "BgCy5.pdf", sep = "_")): unused argument (horiz = F)
principal : save.as.pdf: possible error in pdf(paste(name, "BgCy3.pdf",
  sep = "_"), horiz = F, height = 8, width = 8, title = paste(name,
  "BgCy3.pdf", sep = "_")): unused argument (horiz = F)
principal : save.as.pdf: possible error in pdf(paste(name, "Swap.pdf",
  sep = "_"), horiz = F, height = 8, width = 8, title = paste(name,
  "Swap.pdf", sep = "_")): unused argument (horiz = F)
principal: no visible global function definition for ‘tkrplot’
principal : <anonymous>: no visible global function definition for
  ‘tkrreplot’
Undefined global functions or variables:
  locfit op.counter print.xtable rbox select.experiments tkrplot
  tkrreplot
* 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 ... OK
* 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, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/genArise.Rcheck/00check.log’
for details.

Installation output

genArise.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL genArise
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘genArise’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
Note: possible error in 'pdf(paste(name, ".pdf", ': unused argument (horiz = FALSE) 
Note: possible error in 'pdf(paste(name, ".pdf", ': unused argument (horiz = FALSE) 
Note: possible error in 'pdf(paste(name, "OriginalCy3vsCy5.pdf", ': unused argument (horiz = F) 
Note: possible error in 'pdf(paste(name, "OriginalRvsI.pdf", ': unused argument (horiz = F) 
Note: possible error in 'pdf(paste(name, "OriginalMvsA.pdf", ': unused argument (horiz = F) 
Note: possible error in 'pdf(paste(name, "CorrectedCy3vsCy5.pdf", ': unused argument (horiz = F) 
Note: possible error in 'pdf(paste(name, "CorrectedRvsI.pdf", ': unused argument (horiz = F) 
Note: possible error in 'pdf(paste(name, "CorrectedMvsA.pdf", ': unused argument (horiz = F) 
Note: possible error in 'pdf(paste(name, "NormalCy3vsCy5.pdf", ': unused argument (horiz = F) 
Note: possible error in 'pdf(paste(name, "NormalRvsI.pdf", ': unused argument (horiz = F) 
Note: possible error in 'pdf(paste(name, "NormalMvsA.pdf", ': unused argument (horiz = F) 
Note: possible error in 'pdf(paste(name, "FilterCy3vsCy5.pdf", ': unused argument (horiz = F) 
Note: possible error in 'pdf(paste(name, "FilterRvsI.pdf", ': unused argument (horiz = F) 
Note: possible error in 'pdf(paste(name, "FilterMvsA.pdf", ': unused argument (horiz = F) 
Note: possible error in 'pdf(paste(name, "NoDuplicatesCy3vsCy5.pdf", ': unused argument (horiz = F) 
Note: possible error in 'pdf(paste(name, "NoDuplicatesRvsI.pdf", ': unused argument (horiz = F) 
Note: possible error in 'pdf(paste(name, "NoDuplicatesMvsA.pdf", ': unused argument (horiz = F) 
Note: possible error in 'pdf(paste(name, "OriginalCy3vsCy5.pdf", ': unused argument (horiz = F) 
Note: possible error in 'pdf(paste(name, "OriginalRvsI.pdf", ': unused argument (horiz = F) 
Note: possible error in 'pdf(paste(name, "OriginalMvsA.pdf", ': unused argument (horiz = F) 
Note: possible error in 'pdf(paste(name, "CorrectedCy3vsCy5.pdf", ': unused argument (horiz = F) 
Note: possible error in 'pdf(paste(name, "CorrectedRvsI.pdf", ': unused argument (horiz = F) 
Note: possible error in 'pdf(paste(name, "CorrectedMvsA.pdf", ': unused argument (horiz = F) 
Note: possible error in 'pdf(paste(name, "NormalCy3vsCy5.pdf", ': unused argument (horiz = F) 
Note: possible error in 'pdf(paste(name, "NormalRvsI.pdf", ': unused argument (horiz = F) 
Note: possible error in 'pdf(paste(name, "NormalMvsA.pdf", ': unused argument (horiz = F) 
Note: possible error in 'pdf(paste(name, "FilterCy3vsCy5.pdf", ': unused argument (horiz = F) 
Note: possible error in 'pdf(paste(name, "FilterRvsI.pdf", ': unused argument (horiz = F) 
Note: possible error in 'pdf(paste(name, "FilterMvsA.pdf", ': unused argument (horiz = F) 
Note: possible error in 'pdf(paste(name, "NoDuplicatesCy3vsCy5.pdf", ': unused argument (horiz = F) 
Note: possible error in 'pdf(paste(name, "NoDuplicatesRvsI.pdf", ': unused argument (horiz = F) 
Note: possible error in 'pdf(paste(name, "NoDuplicatesMvsA.pdf", ': unused argument (horiz = F) 
Note: possible error in 'pdf(name, horiz = F, ': unused argument (horiz = F) 
Note: possible error in 'pdf(paste(name, ".pdf", ': unused argument (horiz = FALSE) 
Note: possible error in 'pdf(paste(name, "R&G.pdf", ': unused argument (horiz = F) 
Note: possible error in 'pdf(paste(name, "BgCy5.pdf", ': unused argument (horiz = F) 
Note: possible error in 'pdf(paste(name, "BgCy3.pdf", ': unused argument (horiz = F) 
Note: possible error in 'pdf(paste(name, "Swap.pdf", ': unused argument (horiz = F) 
** help
*** installing help indices
** building package indices
** installing vignettes
** 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
* DONE (genArise)

Tests output

Example timings

genArise.Rcheck/genArise-Ex.timings

nameusersystemelapsed
Simon0.0450.0000.044
WT.dataset0.0900.0120.101
Zscore0.4790.0450.509
Zscore.plot0.1440.0000.143
a.arise0.0050.0000.005
alter.unique0.1130.0080.120
bg.correct0.0050.0000.005
cys.plot0.0900.0040.094
filter.spot0.0800.0250.103
global.norm0.0240.0000.024
grid.norm0.0510.0040.055
i.arise0.0120.0040.015
imageLimma0.0200.0030.024
m.arise0.0030.0000.003
ma.plot0.020.000.02
meanUnique0.1090.0200.125
r.arise0.0030.0000.003
ri.plot0.0240.0000.023
spotUnique0.0780.0160.092
trim0.0010.0000.000
write.dataSet0.0110.0040.014
write.spot0.0180.0040.021
write.zscore0.030.000.03