Gregory C Imholte
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/pepStat |
| Branch: RELEASE_3_8 |
| Last Commit: 3e2b046 |
| Last Changed Date: 2018-10-30 11:41:54 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:24:02 -0400 (Sat, 13 Apr 2019).
| Package 1142/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| pepStat 1.16.0 Gregory C Imholte
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: pepStat |
| Version: 1.16.0 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pepStat.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings pepStat_1.16.0.tar.gz |
| StartedAt: 2019-04-13 04:28:34 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 04:33:10 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 276.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: pepStat.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pepStat.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings pepStat_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/pepStat.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.16.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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'
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'
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'
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'
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'
coerce,peptideSet-ExpressionSet: no visible global function definition
for 'annotation'
end,peptideSet: no visible global function definition for 'end'
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'
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 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 or elapsed time > 5s
user system elapsed
makeCalls 4.17 0.03 5.65
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotArray 6.13 0.06 6.18
makeCalls 6.12 0.01 6.14
restab 5.76 0.04 5.80
summarizePeptides 5.44 0.05 5.49
normalizeArray 5.43 0.01 5.46
slidingMean 5.13 0.01 5.14
* 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-3.8-bioc/meat/pepStat.Rcheck/00check.log'
for details.
pepStat.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/pepStat_1.16.0.tar.gz && rm -rf pepStat.buildbin-libdir && mkdir pepStat.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pepStat.buildbin-libdir pepStat_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL pepStat_1.16.0.zip && rm pepStat_1.16.0.tar.gz pepStat_1.16.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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100 395k 100 395k 0 0 3839k 0 --:--:-- --:--:-- --:--:-- 3991k
install for i386
* installing *source* package 'pepStat' ...
** 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'
** 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
No methods found in package 'GenomicRanges' for request: 'mcols<-' when loading 'pepStat'
No methods found in package 'GenomicRanges' for request: 'mcols' when loading 'pepStat'
In R CMD INSTALL
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'
* MD5 sums
packaged installation of 'pepStat' as pepStat_1.16.0.zip
* DONE (pepStat)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'pepStat' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
pepStat.Rcheck/examples_i386/pepStat-Ex.timings
|
pepStat.Rcheck/examples_x64/pepStat-Ex.timings
|