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###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:genArise.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings genArise_1.59.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/genArise.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.59.0’
* 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-3.9-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-3.9-bioc/meat/genArise.Rcheck/00check.log’
for details.
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###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL genArise
###
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* installing to library ‘/home/biocbuild/bbs-3.9-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)
