Hani Habra
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/metabCombiner |
| Branch: RELEASE_3_12 |
| Last Commit: 6fde963 |
| Last Changed Date: 2020-12-07 15:42:37 -0400 (Mon, 07 Dec 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:32:11 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the metabCombiner package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1045/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| metabCombiner 1.0.1 (landing page) Hani Habra
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: metabCombiner |
| Version: 1.0.1 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metabCombiner.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings metabCombiner_1.0.1.tar.gz |
| StartedAt: 2021-05-06 04:24:41 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 04:29:25 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 284.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: metabCombiner.Rcheck |
| Warnings: 2 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metabCombiner.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings metabCombiner_1.0.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/metabCombiner.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'metabCombiner/DESCRIPTION' ... OK
* this is package 'metabCombiner' version '1.0.1'
* 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 'metabCombiner' 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
metabData: no visible global function definition for 'is'
Undefined global functions or variables:
is
Consider adding
importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic 'getExtra' and siglist 'metabCombiner'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'getExtra':
getExtra
Code: function(object, data = "x")
Docs: function(object, data = c("x", "y"))
Mismatches in argument default values:
Name: 'data' Code: "x" Docs: c("x", "y")
Codoc mismatches from documentation object 'getSamples':
getSamples
Code: function(object, data = "x")
Docs: function(object, data = c("x", "y"))
Mismatches in argument default values:
Name: 'data' Code: "x" Docs: c("x", "y")
\S4method{getSamples}{metabCombiner}
Code: function(object, data = "x")
Docs: function(object, data = c("x", "y"))
Mismatches in argument default values:
Name: 'data' Code: "x" Docs: c("x", "y")
Codoc mismatches from documentation object 'nonmatched':
nonmatched
Code: function(object, data = "x")
Docs: function(object, data = c("x", "y"))
Mismatches in argument default values:
Name: 'data' Code: "x" Docs: c("x", "y")
\S4method{nonmatched}{metabCombiner}
Code: function(object, data = "x")
Docs: function(object, data = c("x", "y"))
Mismatches in argument default values:
Name: 'data' Code: "x" Docs: c("x", "y")
* 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 data for ASCII and uncompressed saves ... 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-3.12-bioc/R/library/metabCombiner/libs/i386/metabCombiner.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/metabCombiner/libs/x64/metabCombiner.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
calcScores 14.56 0.11 14.67
evaluateParams 5.36 0.02 5.38
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
calcScores 14.98 0.05 15.03
evaluateParams 7.25 0.03 7.28
write2file 5.71 0.02 5.72
* 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 WARNINGs, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/metabCombiner.Rcheck/00check.log'
for details.
metabCombiner.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/metabCombiner_1.0.1.tar.gz && rm -rf metabCombiner.buildbin-libdir && mkdir metabCombiner.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=metabCombiner.buildbin-libdir metabCombiner_1.0.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL metabCombiner_1.0.1.zip && rm metabCombiner_1.0.1.tar.gz metabCombiner_1.0.1.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 804k 100 804k 0 0 13.8M 0 --:--:-- --:--:-- --:--:-- 14.2M
install for i386
* installing *source* package 'metabCombiner' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c binByMZ.c -o binByMZ.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c findDuplicates.c -o findDuplicates.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c labelRows.c -o labelRows.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c metabCombiner_init.c -o metabCombiner_init.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c selectAnchors.c -o selectAnchors.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c write2file.c -o write2file.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o metabCombiner.dll tmp.def binByMZ.o findDuplicates.o labelRows.o metabCombiner_init.o selectAnchors.o write2file.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/metabCombiner.buildbin-libdir/00LOCK-metabCombiner/00new/metabCombiner/libs/i386
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'metabCombiner'
finding HTML links ... done
adjustData html
calcScores html
combinedTable html
combinerCheck html
crossValFit html
detectFields html
evaluateParams html
filterAnchors html
filterRT html
findDuplicates html
fit_gam html
fit_loess html
formCombinedTable html
getAnchors html
getCoefficients html
getData html
getExtra html
getModel html
getSamples html
getStats html
identityAnchorSelection html
isCombinedTable html
isMetabCombiner html
isMetabData html
iterativeAnchorSelection html
labelRows html
metabCombiner-class html
metabCombiner html
metabData-class html
metabData html
mzGroup html
nonmatched html
objective html
plasma20 html
plasma30 html
plot_fit html
scorePairs html
selectAnchors html
write2file 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 'metabCombiner' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c binByMZ.c -o binByMZ.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c findDuplicates.c -o findDuplicates.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c labelRows.c -o labelRows.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c metabCombiner_init.c -o metabCombiner_init.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c selectAnchors.c -o selectAnchors.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c write2file.c -o write2file.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o metabCombiner.dll tmp.def binByMZ.o findDuplicates.o labelRows.o metabCombiner_init.o selectAnchors.o write2file.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/metabCombiner.buildbin-libdir/metabCombiner/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'metabCombiner' as metabCombiner_1.0.1.zip
* DONE (metabCombiner)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'metabCombiner' successfully unpacked and MD5 sums checked
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metabCombiner.Rcheck/tests_i386/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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(metabCombiner)
Loading required package: dplyr
Attaching package: 'dplyr'
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
>
> test_check("metabCombiner")
Performing filtering iteration: 1
Performing filtering iteration: 2
Performing 10-fold cross validation
Fitting Model with k = 18
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 31 ]
>
> proc.time()
user system elapsed
13.17 0.60 13.76
|
metabCombiner.Rcheck/tests_x64/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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(metabCombiner)
Loading required package: dplyr
Attaching package: 'dplyr'
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
>
> test_check("metabCombiner")
Performing filtering iteration: 1
Performing filtering iteration: 2
Performing 10-fold cross validation
Fitting Model with k = 18
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 31 ]
>
> proc.time()
user system elapsed
16.01 0.53 16.53
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metabCombiner.Rcheck/examples_i386/metabCombiner-Ex.timings
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metabCombiner.Rcheck/examples_x64/metabCombiner-Ex.timings
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