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This page was generated on 2021-10-15 15:06:22 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the scRepertoire package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scRepertoire.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1715/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scRepertoire 1.2.0 (landing page) Nick Borcherding
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: scRepertoire |
| Version: 1.2.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scRepertoire.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings scRepertoire_1.2.0.tar.gz |
| StartedAt: 2021-10-15 05:22:02 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 05:31:02 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 539.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: scRepertoire.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scRepertoire.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings scRepertoire_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/scRepertoire.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'scRepertoire/DESCRIPTION' ... OK
* this is package 'scRepertoire' version '1.2.0'
* package encoding: UTF-8
* 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 'scRepertoire' can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.1Mb
sub-directories of 1Mb or more:
data 4.4Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... 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
clonesizeDistribution 16.31 0.33 16.64
alluvialClonotypes 11.90 0.66 12.54
abundanceContig 9.31 0.22 9.53
combineTCR 7.97 0.47 8.44
combineExpression 7.77 0.00 7.76
occupiedscRepertoire 7.20 0.00 7.21
clonalDiversity 6.46 0.08 6.55
addVariable 6.41 0.09 6.50
expression2List 6.47 0.00 6.46
clonalProportion 6.19 0.00 6.19
compareClonotypes 6.12 0.00 6.13
quantContig 6.08 0.00 6.07
vizVgenes 6.03 0.00 6.03
lengthContig 5.90 0.00 5.90
clonalHomeostasis 5.85 0.03 5.88
highlightClonotypes 5.85 0.00 5.85
getCirclize 5.81 0.01 5.83
subsetContig 5.72 0.01 5.73
combineBCR 5.50 0.14 5.86
clonalOverlap 5.45 0.03 5.48
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
clonesizeDistribution 17.64 0.02 17.65
alluvialClonotypes 12.03 0.29 12.33
clonalHomeostasis 9.73 0.00 9.75
occupiedscRepertoire 8.41 0.01 8.42
clonalOverlap 8.38 0.00 8.39
combineTCR 7.92 0.41 8.33
abundanceContig 8.12 0.06 8.19
combineExpression 7.77 0.00 7.77
vizVgenes 7.58 0.00 7.58
expression2List 7.36 0.00 7.36
addVariable 7.33 0.02 7.34
clonalDiversity 7.21 0.02 7.23
getCirclize 7.19 0.00 7.19
lengthContig 6.89 0.00 6.89
clonalProportion 6.59 0.00 6.60
highlightClonotypes 6.34 0.02 6.36
quantContig 6.34 0.00 6.35
subsetContig 6.27 0.02 6.28
compareClonotypes 6.05 0.00 6.04
combineBCR 5.20 0.07 5.42
* 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 NOTE
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/scRepertoire.Rcheck/00check.log'
for details.
scRepertoire.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/scRepertoire_1.2.0.tar.gz && rm -rf scRepertoire.buildbin-libdir && mkdir scRepertoire.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scRepertoire.buildbin-libdir scRepertoire_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL scRepertoire_1.2.0.zip && rm scRepertoire_1.2.0.tar.gz scRepertoire_1.2.0.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
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
95 3763k 95 3585k 0 0 3567k 0 0:00:01 0:00:01 --:--:-- 3567k
100 3763k 100 3763k 0 0 3612k 0 0:00:01 0:00:01 --:--:-- 3611k
install for i386
* installing *source* package 'scRepertoire' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'scRepertoire'
finding HTML links ... done
Startrac html
Startrac.run html
StartracDiversity html
StartracOut html
abundanceContig html
addVariable html
alluvialClonotypes html
calIndex html
clonalDiversity html
clonalHomeostasis html
clonalOverlap html
clonalProportion html
clonesizeDistribution html
combineBCR html
combineExpression html
combineTCR html
compareClonotypes html
contig_list html
expression2List html
getCirclize html
getSig html
highlightClonotypes html
initialize-StartracOut-method html
initialize-methods html
lengthContig html
loginfo html
mcol.entropy html
mrow.entropy html
occupiedscRepertoire html
pIndex html
quantContig html
screp_example html
show-StartracOut-method html
show html
stripBarcode html
subsetContig html
vizVgenes html
** 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
install for x64
* installing *source* package 'scRepertoire' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scRepertoire' as scRepertoire_1.2.0.zip
* DONE (scRepertoire)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'scRepertoire' successfully unpacked and MD5 sums checked
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scRepertoire.Rcheck/examples_i386/scRepertoire-Ex.timings
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scRepertoire.Rcheck/examples_x64/scRepertoire-Ex.timings
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