Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-04-12 11:05:34 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 genArise on palomino4


To the developers/maintainers of the genArise package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/genArise.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 749/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genArise 1.74.0  (landing page)
IFC Development Team
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/genArise
git_branch: RELEASE_3_16
git_last_commit: 03467e9
git_last_commit_date: 2022-11-01 10:37:53 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: genArise
Version: 1.74.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:genArise.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings genArise_1.74.0.tar.gz
StartedAt: 2023-04-11 01:43:28 -0400 (Tue, 11 Apr 2023)
EndedAt: 2023-04-11 01:44:13 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 45.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: genArise.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:genArise.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings genArise_1.74.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/genArise.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'genArise/DESCRIPTION' ... OK
* this is package 'genArise' version '1.74.0'
* 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 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 'F:/biocbuild/bbs-3.16-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 sizes of PDF files under 'inst/doc' ... 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
  'F:/biocbuild/bbs-3.16-bioc/meat/genArise.Rcheck/00check.log'
for details.



Installation output

genArise.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL genArise
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.16-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
Simon0.030.000.03
WT.dataset0.030.020.05
Zscore0.270.000.26
Zscore.plot0.090.000.10
a.arise000
alter.unique0.070.020.07
bg.correct000
cys.plot0.070.000.08
filter.spot0.080.060.14
global.norm0.020.020.03
grid.norm0.030.000.04
i.arise0.000.010.01
imageLimma0.010.000.01
m.arise000
ma.plot0.020.010.03
meanUnique0.080.020.10
r.arise000
ri.plot0.010.010.03
spotUnique0.070.040.09
trim000
write.dataSet0.040.010.08
write.spot0.020.000.03
write.zscore0.030.020.03