Matthias Lienhard
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/qsea |
| git_branch: RELEASE_3_13 |
| git_last_commit: f23006b |
| git_last_commit_date: 2021-05-19 12:21:24 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:17 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the qsea package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/qsea.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 1476/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| qsea 1.18.0 (landing page) Matthias Lienhard
| 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: qsea |
| Version: 1.18.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:qsea.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings qsea_1.18.0.tar.gz |
| StartedAt: 2021-10-15 03:58:58 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 04:05:37 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 399.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: qsea.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:qsea.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings qsea_1.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/qsea.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 'qsea/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'qsea' version '1.18.0'
* 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 'qsea' 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 ... NOTE
Namespaces in Imports field not imported from:
'KernSmooth' 'MASS'
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
subdivideRegions: no visible global function definition for 'metadata'
Undefined global functions or variables:
metadata
* 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 R/sysdata.rda ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/qsea/libs/i386/qsea.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/qsea/libs/x64/qsea.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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
addNewSamples 20.86 2.71 25.35
addCNV 6.94 0.85 9.58
addPatternDensity 7.37 0.35 7.72
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
addNewSamples 17.58 0.38 17.96
addPatternDensity 7.90 0.16 8.07
addCNV 6.89 0.14 7.03
* 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: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/qsea.Rcheck/00check.log'
for details.
qsea.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/qsea_1.18.0.tar.gz && rm -rf qsea.buildbin-libdir && mkdir qsea.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=qsea.buildbin-libdir qsea_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL qsea_1.18.0.zip && rm qsea_1.18.0.tar.gz qsea_1.18.0.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
17 284k 17 49977 0 0 240k 0 0:00:01 --:--:-- 0:00:01 240k
100 284k 100 284k 0 0 1015k 0 --:--:-- --:--:-- --:--:-- 1013k
install for i386
* installing *source* package 'qsea' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c lm.c -o lm.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o qsea.dll tmp.def lm.o -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/qsea.buildbin-libdir/00LOCK-qsea/00new/qsea/libs/i386
** R
** inst
** preparing package for lazy loading
No methods found in package 'IRanges' for request: 'values' when loading 'qsea'
** help
*** installing help indices
converting help for package 'qsea'
finding HTML links ... done
addCNV html
addContrast html
addCoverage html
addEnrichmentParameters html
addLibraryFactors html
addNewSamples html
addOffset html
addPatternDensity html
addSeqPref html
createQseaSet html
example html
fitNBglm html
getPCA html
isSignificant html
makeTable html
normMethod html
plotCNV html
plotCoverage html
plotEnrichmentProfile html
plotPCA html
qsea-package html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/qsea.buildbin-libdir/00LOCK-qsea/00new/qsea/help/QSEA.html
qseaGLM-class html
qseaPCA-class html
qseaSet-class html
regionStats html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package 'IRanges' for request: 'values' when loading 'qsea'
** testing if installed package can be loaded from final location
No methods found in package 'IRanges' for request: 'values' when loading 'qsea'
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'qsea' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c lm.c -o lm.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o qsea.dll tmp.def lm.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/qsea.buildbin-libdir/qsea/libs/x64
** testing if installed package can be loaded
No methods found in package 'IRanges' for request: 'values' when loading 'qsea'
* MD5 sums
packaged installation of 'qsea' as qsea_1.18.0.zip
* DONE (qsea)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'qsea' successfully unpacked and MD5 sums checked
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qsea.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(qsea)
No methods found in package 'IRanges' for request: 'values' when loading 'qsea'
>
> test_check("qsea")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]
>
> proc.time()
user system elapsed
10.54 0.95 11.48
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qsea.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(qsea)
No methods found in package 'IRanges' for request: 'values' when loading 'qsea'
>
> test_check("qsea")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]
>
> proc.time()
user system elapsed
11.17 0.46 11.62
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qsea.Rcheck/examples_i386/qsea-Ex.timings
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qsea.Rcheck/examples_x64/qsea-Ex.timings
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