Vivek Bhardwaj
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/icetea |
| git_branch: RELEASE_3_13 |
| git_last_commit: b536bec |
| git_last_commit_date: 2021-05-19 12:36:20 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:08 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the icetea package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/icetea.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 893/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| icetea 1.10.0 (landing page) Vivek Bhardwaj
| 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: icetea |
| Version: 1.10.0 |
| Command: set _R_CHECK_FORCE_SUGGESTS_=0&& C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:icetea.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings icetea_1.10.0.tar.gz |
| StartedAt: 2021-10-15 00:34:54 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 00:48:22 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 807.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: icetea.Rcheck |
| Warnings: 0 |
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### Running command:
###
### set _R_CHECK_FORCE_SUGGESTS_=0&& C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:icetea.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings icetea_1.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/icetea.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 'icetea/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'icetea' version '1.10.0'
* 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 'icetea' can be installed ... OK
* checking installed package size ... OK
* 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
detectTSS,CapSet : <anonymous>: no visible binding for global variable
'logFC'
fitDiffTSS,CapSet: no visible binding for global variable 'ResizeReads'
Undefined global functions or variables:
ResizeReads logFC
* 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 (user + system) or elapsed time > 5s
user system elapsed
detectTSS 14.95 1.45 28.83
annotateTSS 11.83 0.88 112.22
demultiplexFASTQ 2.12 0.03 18.16
getNormFactors 1.78 0.22 36.53
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
detectTSS 14.14 1.40 29.81
annotateTSS 9.16 0.10 9.34
getNormFactors 1.86 0.03 41.87
* 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: 1 NOTE
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/icetea.Rcheck/00check.log'
for details.
icetea.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/icetea_1.10.0.tar.gz && rm -rf icetea.buildbin-libdir && mkdir icetea.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=icetea.buildbin-libdir icetea_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL icetea_1.10.0.zip && rm icetea_1.10.0.tar.gz icetea_1.10.0.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 1263k 100 1263k 0 0 2285k 0 --:--:-- --:--:-- --:--:-- 2289k
install for i386
* installing *source* package 'icetea' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'icetea'
finding HTML links ... done
activeChrs html
annotateTSS html
check_capSet html
demultiplexFASTQ html
detectDiffTSS html
finding level-2 HTML links ... done
detectTSS html
diffQCplots html
exampleCSobject html
exportTSS html
filterDuplicates html
filterDups html
fitDiffTSS html
getBamFlags html
getChromBins html
getChromWindows html
getGeneCounts html
getMCparams html
getNormFactors html
get_newfastq html
getranks html
mapCaps html
newCapSet html
numReadsInBed html
plotPrecision html
plotReadStats html
plotTSSprecision html
readsTo3p html
readsTo5p html
readsToCenter html
sampleInfo html
splitBAM_byIndex html
splitBAM_byRepindex html
split_fastq html
splitranks html
strandBinCounts 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 'icetea' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'icetea' as icetea_1.10.0.zip
* DONE (icetea)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'icetea' successfully unpacked and MD5 sums checked
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icetea.Rcheck/tests_i386/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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(icetea)
>
> test_check("icetea")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 17 ]
>
> proc.time()
user system elapsed
38.18 3.32 66.40
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icetea.Rcheck/tests_x64/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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(icetea)
>
> test_check("icetea")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 17 ]
>
> proc.time()
user system elapsed
37.42 1.82 60.06
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icetea.Rcheck/examples_i386/icetea-Ex.timings
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icetea.Rcheck/examples_x64/icetea-Ex.timings
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