Jeffrey T. Leek
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/sva |
| Branch: RELEASE_3_9 |
| Last Commit: 1b82867 |
| Last Changed Date: 2019-05-22 11:08:55 -0400 (Wed, 22 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:49:30 -0400 (Wed, 16 Oct 2019).
| Package 1613/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| sva 3.32.1 Jeffrey T. Leek
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: sva |
| Version: 3.32.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:sva.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings sva_3.32.1.tar.gz |
| StartedAt: 2019-10-16 07:15:30 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 07:19:47 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 257.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: sva.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:sva.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings sva_3.32.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/sva.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sva/DESCRIPTION’ ... OK
* this is package ‘sva’ version ‘3.32.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘sva’ 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
* 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
sva_network: no visible global function definition for ‘lm’
Undefined global functions or variables:
lm
Consider adding
importFrom("stats", "lm")
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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
sva.check 9.794 0.959 10.800
sva_network 8.133 0.706 8.842
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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
‘/Users/biocbuild/bbs-3.9-bioc/meat/sva.Rcheck/00check.log’
for details.
sva.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL sva
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘sva’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c sva.c -o sva.o
sva.c:29:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
NULL
^~~~
{ }
/usr/local/clang4/bin/../lib/clang/4.0.0/include/stddef.h:105:16: note: expanded from macro 'NULL'
# define NULL ((void*)0)
^~~~~~~~~~
1 warning generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o sva.so sva.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-sva/00new/sva/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (sva)
sva.Rcheck/tests/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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(sva)
Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-29. For overview type 'help("mgcv-package")'.
Loading required package: genefilter
Loading required package: BiocParallel
>
> test_check("sva")
Standardizing Data across genes
Standardizing Data across genes
Standardizing Data across genes
Standardizing Data across genes
Standardizing Data across genes
Standardizing Data across genes
Using batch = 1 as a reference batch (this batch won't change)
Standardizing Data across genes
Using batch = 3 as a reference batch (this batch won't change)
Standardizing Data across genes
Standardizing Data across genes
Standardizing Data across genes
Standardizing Data across genes
Standardizing Data across genes
Standardizing Data across genes
Standardizing Data across genes
Standardizing Data across genes
Standardizing Data across genes
Standardizing Data across genes
Standardizing Data across genes
Using batch = 1 as a reference batch (this batch won't change)
Standardizing Data across genes
Using batch = 3 as a reference batch (this batch won't change)
Standardizing Data across genes
Standardizing Data across genes
Standardizing Data across genes
Standardizing Data across genes
Standardizing Data across genes
Standardizing Data across genes
Standardizing Data across genes
Standardizing Data across genes
Standardizing Data across genes
Using batch = 1 as a reference batch (this batch won't change)
Standardizing Data across genes
Using batch = 2 as a reference batch (this batch won't change)
Standardizing Data across genes
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 30 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
34.920 13.520 45.323
sva.Rcheck/sva-Ex.timings
| name | user | system | elapsed | |
| ComBat | 1.637 | 0.083 | 1.725 | |
| empirical.controls | 2.185 | 0.197 | 2.382 | |
| f.pvalue | 0.366 | 0.041 | 0.406 | |
| fstats | 0.387 | 0.041 | 0.428 | |
| fsva | 0.694 | 0.059 | 0.756 | |
| irwsva.build | 1.559 | 0.122 | 1.681 | |
| num.sv | 0.973 | 0.068 | 1.041 | |
| psva | 0.509 | 0.025 | 0.533 | |
| qsva | 1.282 | 0.580 | 1.545 | |
| read.degradation.matrix | 2.659 | 1.466 | 2.711 | |
| ssva | 0.823 | 0.152 | 0.974 | |
| sva | 1.657 | 0.196 | 1.853 | |
| sva.check | 9.794 | 0.959 | 10.800 | |
| sva_network | 8.133 | 0.706 | 8.842 | |
| svaseq | 0.782 | 0.170 | 0.954 | |
| twostepsva.build | 4.241 | 0.497 | 4.741 | |