Charlotte Soneson
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/alevinQC |
| Branch: RELEASE_3_10 |
| Last Commit: 8ca336f |
| Last Changed Date: 2019-10-29 13:11:30 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:31:51 -0400 (Wed, 15 Apr 2020).
| Package 42/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| alevinQC 1.2.0 Charlotte Soneson
| malbec1 | Linux (Ubuntu 18.04.4 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: alevinQC |
| Version: 1.2.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:alevinQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings alevinQC_1.2.0.tar.gz |
| StartedAt: 2020-04-15 01:13:22 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 01:16:23 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 181.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: alevinQC.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:alevinQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings alevinQC_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/alevinQC.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'alevinQC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'alevinQC' 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 'alevinQC' can be installed ... OK
* checking installed package size ... NOTE
installed size is 11.7Mb
sub-directories of 1Mb or more:
extdata 11.6Mb
* 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 ... NOTE
.readAlevinQC_pre0.14: no visible binding for global variable 'V1'
.readAlevinQC_pre0.14: no visible binding for global variable 'V2'
.readAlevinQC_pre0.14: no visible binding for global variable 'CB'
.readAlevinQC_pre0.14: no visible binding for global variable 'V3'
.readAlevinQC_pre0.14: no visible binding for global variable 'V4'
.readAlevinQC_pre0.14: no visible binding for global variable 'V5'
.readAlevinQC_pre0.14: no visible binding for global variable
'inFirstWhiteList'
.readAlevinQC_pre0.14: no visible binding for global variable
'inFinalWhiteList'
.readAlevinQC_v0.14: no visible binding for global variable 'V1'
.readAlevinQC_v0.14: no visible binding for global variable 'V2'
.readAlevinQC_v0.14: no visible binding for global variable 'CB'
.readAlevinQC_v0.14: no visible binding for global variable
'MappingRate'
.readAlevinQC_v0.14: no visible binding for global variable
'CorrectedReads'
.readAlevinQC_v0.14: no visible binding for global variable 'DedupRate'
.readAlevinQC_v0.14: no visible binding for global variable
'NumGenesOverMean'
.readAlevinQC_v0.14: no visible binding for global variable
'MappedReads'
.readAlevinQC_v0.14: no visible binding for global variable
'DeduplicatedReads'
.readAlevinQC_v0.14: no visible binding for global variable
'NumGenesExpressed'
.readAlevinQC_v0.14: no visible binding for global variable 'ranking'
plotAlevinBarcodeCollapse: no visible binding for global variable
'inFirstWhiteList'
plotAlevinBarcodeCollapse: no visible binding for global variable
'collapsedFreq'
plotAlevinBarcodeCollapse: no visible binding for global variable
'originalFreq'
plotAlevinKneeNbrGenes: no visible binding for global variable
'inFirstWhiteList'
plotAlevinKneeNbrGenes: no visible binding for global variable
'nbrGenesAboveZero'
plotAlevinKneeNbrGenes: no visible binding for global variable 'x'
plotAlevinKneeRaw: no visible binding for global variable 'ranking'
plotAlevinKneeRaw: no visible binding for global variable
'originalFreq'
plotAlevinKneeRaw: no visible binding for global variable
'inFirstWhiteList'
plotAlevinQuant: no visible binding for global variable
'inFirstWhiteList'
plotAlevinQuant: no visible binding for global variable 'collapsedFreq'
plotAlevinQuant: no visible binding for global variable 'totalUMICount'
plotAlevinQuant: no visible binding for global variable
'inFinalWhiteList'
plotAlevinQuant: no visible binding for global variable
'nbrGenesAboveZero'
plotAlevinQuantPairs: no visible binding for global variable
'inFirstWhiteList'
plotAlevinQuantPairs: no visible binding for global variable
'inFinalWhiteList'
Undefined global functions or variables:
CB CorrectedReads DedupRate DeduplicatedReads MappedReads MappingRate
NumGenesExpressed NumGenesOverMean V1 V2 V3 V4 V5 collapsedFreq
inFinalWhiteList inFirstWhiteList nbrGenesAboveZero originalFreq
ranking totalUMICount x
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
alevinQCReport 9.16 0.93 11.55
plotAlevinKneeRaw 5.83 0.88 6.70
plotAlevinBarcodeCollapse 4.01 0.44 5.32
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
alevinQCReport 8.63 0.77 10.03
plotAlevinKneeRaw 6.73 0.80 7.53
plotAlevinQuantPairs 5.63 0.39 6.02
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/alevinQC.Rcheck/00check.log'
for details.
alevinQC.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/alevinQC_1.2.0.tar.gz && rm -rf alevinQC.buildbin-libdir && mkdir alevinQC.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=alevinQC.buildbin-libdir alevinQC_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL alevinQC_1.2.0.zip && rm alevinQC_1.2.0.tar.gz alevinQC_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
100 5727k 100 5727k 0 0 59.3M 0 --:--:-- --:--:-- --:--:-- 62.1M
install for i386
* installing *source* package 'alevinQC' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'alevinQC'
finding HTML links ... done
alevinQCReport html
alevinQCShiny html
checkAlevinInputFiles html
plotAlevinBarcodeCollapse html
plotAlevinKneeNbrGenes html
plotAlevinKneeRaw html
plotAlevinQuant html
plotAlevinQuantPairs html
readAlevinQC 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 'alevinQC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'alevinQC' as alevinQC_1.2.0.zip
* DONE (alevinQC)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'alevinQC' successfully unpacked and MD5 sums checked
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alevinQC.Rcheck/tests_i386/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(alevinQC)
>
> test_check("alevinQC")
== testthat results ===========================================================
[ OK: 40 | SKIPPED: 0 | WARNINGS: 7 | FAILED: 0 ]
>
> proc.time()
user system elapsed
25.56 3.62 30.23
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alevinQC.Rcheck/tests_x64/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(alevinQC)
>
> test_check("alevinQC")
== testthat results ===========================================================
[ OK: 40 | SKIPPED: 0 | WARNINGS: 7 | FAILED: 0 ]
>
> proc.time()
user system elapsed
27.17 3.56 31.81
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alevinQC.Rcheck/examples_i386/alevinQC-Ex.timings
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alevinQC.Rcheck/examples_x64/alevinQC-Ex.timings
|