##############################################################################
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:genArise.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings genArise_1.56.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/genArise.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'genArise/DESCRIPTION' ... OK
* this is package 'genArise' version '1.56.0'
* 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 'C:/Users/biocbuild/bbs-3.7-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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
'C:/Users/biocbuild/bbs-3.7-bioc/meat/genArise.Rcheck/00check.log'
for details.
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/genArise_1.56.0.tar.gz && rm -rf genArise.buildbin-libdir && mkdir genArise.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=genArise.buildbin-libdir genArise_1.56.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL genArise_1.56.0.zip && rm genArise_1.56.0.tar.gz genArise_1.56.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 165k 100 165k 0 0 2512k 0 --:--:-- --:--:-- --:--:-- 2796k
install for i386
* installing *source* package 'genArise' ...
** 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
converting help for package 'genArise'
finding HTML links ... done
DataSet-class html
Simon html
Spot-class html
WT.dataset html
Zscore html
Zscore.plot html
Zscore.points html
a.arise html
alter.unique html
analysis.window html
annotations html
back.gui html
bg.correct html
classes html
create.project html
cys.plot html
filter.spot html
genArise html
genArise.init html
genMerge html
get.Zscore html
get.values html
global.norm html
graphic.choose html
grid.norm html
help html
i.arise html
imageLimma html
m.arise html
ma.plot html
make.swap html
meanUnique html
note html
old.project html
post.analysis html
principal html
projects.select html
r.arise html
read.dataset html
read.spot html
reset.history html
ri.plot html
set.grid.properties html
set.history.project html
set.path.project html
set.project.properties html
single.norm html
spotUnique html
swap.select html
trim html
write.dataSet html
write.spot html
write.zscore html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'genArise' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'genArise' as genArise_1.56.0.zip
* DONE (genArise)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'genArise' successfully unpacked and MD5 sums checked
In R CMD INSTALL
