Gregory C Imholte
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/pepStat |
| Branch: RELEASE_3_12 |
| Last Commit: edd0354 |
| Last Changed Date: 2020-10-27 10:57:24 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:32:44 -0400 (Thu, 06 May 2021).
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To the developers/maintainers of the pepStat package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1326/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| pepStat 1.24.0 (landing page) Gregory C Imholte
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: pepStat |
| Version: 1.24.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pepStat.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings pepStat_1.24.0.tar.gz |
| StartedAt: 2021-05-06 05:27:03 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 05:31:02 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 239.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: pepStat.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pepStat.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings pepStat_1.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/pepStat.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'pepStat/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pepStat' version '1.24.0'
* 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 'pepStat' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
Warning: no function found corresponding to methods exports from 'pepStat' for: 'end', 'start', 'values'
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
** 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 ... NOTE
Warning: no function found corresponding to methods exports from 'pepStat' for: 'end', 'start', 'values'
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.findFDR : <anonymous>: no visible global function definition for
'median'
.sanitize_mapping_file2: no visible global function definition for
'read.csv'
create_db: no visible global function definition for 'mcols<-'
create_db: no visible global function definition for 'mcols'
getPlotCoords: no visible global function definition for 'values'
getWeightedEstimator : <anonymous>: no visible global function
definition for 'lm.fit'
getWeightedEstimator : <anonymous>: no visible global function
definition for 'lm.wfit'
getWeightedEstimator : <anonymous> : <anonymous>: no visible global
function definition for 'sd'
getZpep: no visible global function definition for 'values'
getZpep : <anonymous>: no visible global function definition for
'values'
plotArrayImage: no visible global function definition for
'dev.interactive'
plotArrayImage: no visible global function definition for
'devAskNewPage'
plotArrayImage: no visible global function definition for 'dev.hold'
plotArrayImage: no visible global function definition for 'dev.flush'
plotArrayResiduals: no visible global function definition for
'dev.interactive'
plotArrayResiduals: no visible global function definition for
'devAskNewPage'
plotArrayResiduals: no visible global function definition for
'dev.hold'
plotArrayResiduals: no visible global function definition for
'dev.flush'
summarizePeptides: no visible global function definition for 'values<-'
summarizePeptides: no visible global function definition for 'values'
coerce,peptideSet-ExpressionSet: no visible global function definition
for 'annotation'
end,peptideSet: no visible global function definition for 'end'
featureID,peptideSet: no visible global function definition for
'values'
pepZscore,GRanges: no visible global function definition for 'values'
peptide,peptideSet: no visible global function definition for 'values'
peptide<-,peptideSet-character: no visible global function definition
for 'values'
peptide<-,peptideSet-character: no visible global function definition
for 'values<-'
position,peptideSet: no visible global function definition for 'start'
position,peptideSet: no visible global function definition for 'end'
start,peptideSet: no visible global function definition for 'start'
values,peptideSet: no visible global function definition for 'values'
values<-,peptideSet: no visible global function definition for
'values<-'
write.pSet,peptideSet: no visible global function definition for
'start'
write.pSet,peptideSet: no visible global function definition for 'end'
write.pSet,peptideSet: no visible global function definition for
'write.csv'
Undefined global functions or variables:
annotation dev.flush dev.hold dev.interactive devAskNewPage end
lm.fit lm.wfit mcols mcols<- median read.csv sd start values values<-
write.csv
Consider adding
importFrom("grDevices", "dev.flush", "dev.hold", "dev.interactive",
"devAskNewPage")
importFrom("stats", "end", "lm.fit", "lm.wfit", "median", "sd",
"start")
importFrom("utils", "read.csv", "write.csv")
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
makeCalls 6.66 0.16 7.97
plotArray 5.95 0.05 6.00
normalizeArray 5.67 0.06 5.73
slidingMean 5.47 0.03 5.50
restab 5.23 0.03 5.26
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotArray 6.35 0.00 6.34
makeCalls 6.19 0.04 6.23
summarizePeptides 5.58 0.05 5.62
slidingMean 5.54 0.02 5.56
normalizeArray 5.51 0.00 5.52
* 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: 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/pepStat.Rcheck/00check.log'
for details.
pepStat.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/pepStat_1.24.0.tar.gz && rm -rf pepStat.buildbin-libdir && mkdir pepStat.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pepStat.buildbin-libdir pepStat_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL pepStat_1.24.0.zip && rm pepStat_1.24.0.tar.gz pepStat_1.24.0.zip
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100 395k 100 395k 0 0 22.8M 0 --:--:-- --:--:-- --:--:-- 24.1M
install for i386
* installing *source* package 'pepStat' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'GenomicRanges' for request: 'mcols<-' when loading 'pepStat'
No methods found in package 'GenomicRanges' for request: 'mcols' when loading 'pepStat'
No methods found in package 'IRanges' for request: 'values<-' when loading 'pepStat'
No methods found in package 'IRanges' for request: 'values' when loading 'pepStat'
** help
*** installing help indices
converting help for package 'pepStat'
finding HTML links ... done
baselineCorrect.pSet html
baseline_correct html
create_db html
finding level-2 HTML links ... done
makeCalls html
makePeptideSet html
normalizeArray html
peptideSet-methods html
peptideSet html
plotArray html
restab html
shinyPepStat html
slidingMean html
summarizePeptides html
** building package indices
** installing vignettes
'pepStat.Rnw'
** testing if installed package can be loaded from temporary location
No methods found in package 'GenomicRanges' for request: 'mcols<-' when loading 'pepStat'
No methods found in package 'GenomicRanges' for request: 'mcols' when loading 'pepStat'
No methods found in package 'IRanges' for request: 'values<-' when loading 'pepStat'
No methods found in package 'IRanges' for request: 'values' when loading 'pepStat'
** testing if installed package can be loaded from final location
No methods found in package 'GenomicRanges' for request: 'mcols<-' when loading 'pepStat'
No methods found in package 'GenomicRanges' for request: 'mcols' when loading 'pepStat'
No methods found in package 'IRanges' for request: 'values<-' when loading 'pepStat'
No methods found in package 'IRanges' for request: 'values' when loading 'pepStat'
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'pepStat' ...
** testing if installed package can be loaded
No methods found in package 'GenomicRanges' for request: 'mcols<-' when loading 'pepStat'
No methods found in package 'GenomicRanges' for request: 'mcols' when loading 'pepStat'
No methods found in package 'IRanges' for request: 'values<-' when loading 'pepStat'
No methods found in package 'IRanges' for request: 'values' when loading 'pepStat'
* MD5 sums
packaged installation of 'pepStat' as pepStat_1.24.0.zip
* DONE (pepStat)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'pepStat' successfully unpacked and MD5 sums checked
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pepStat.Rcheck/examples_i386/pepStat-Ex.timings
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pepStat.Rcheck/examples_x64/pepStat-Ex.timings
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