Sebastian Bauer
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/mgsa |
| git_branch: RELEASE_3_13 |
| git_last_commit: 77f80bf |
| git_last_commit_date: 2021-05-19 11:47:06 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:11 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the mgsa package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mgsa.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 1123/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| mgsa 1.40.0 (landing page) Sebastian Bauer
| 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: mgsa |
| Version: 1.40.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mgsa.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings mgsa_1.40.0.tar.gz |
| StartedAt: 2021-10-15 01:52:10 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 01:53:39 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 88.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: mgsa.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:mgsa.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings mgsa_1.40.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/mgsa.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 'mgsa/DESCRIPTION' ... OK
* this is package 'mgsa' version '1.40.0'
* 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 'mgsa' 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 ... NOTE
Warning: no function found corresponding to methods exports from 'mgsa' for: 'show'
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
** 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 ... NOTE
Warning: no function found corresponding to methods exports from 'mgsa' for: 'show'
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to 'gplots' which was already attached by Depends.
Please remove these calls from your code.
'library' or 'require' calls in package code:
'DBI' 'GO.db' 'RSQLite'
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespaces in Imports field not imported from:
'stats' 'utils'
All declared Imports should be used.
Packages in Depends field not imported from:
'gplots' 'methods'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
createMgsaGoSets: no visible global function definition for 'new'
mcmcSummary: no visible binding for global variable 'sd'
mgsa.wrapper: no visible global function definition for 'str'
mgsa.wrapper: no visible global function definition for 'new'
readGAF: no visible global function definition for 'read.delim'
readGAF: no visible global function definition for 'na.omit'
readGAF: no visible global function definition for 'new'
initialize,MgsaSets: no visible global function definition for
'callNextMethod'
initialize,MgsaSets: no visible global function definition for 'relist'
mgsa,character-MgsaSets: no visible global function definition for
'na.omit'
plot,MgsaResults: no visible global function definition for
'split.screen'
plot,MgsaResults: no visible global function definition for 'screen'
plot,MgsaResults: no visible global function definition for 'par'
plot,MgsaResults: no visible global function definition for 'barplot2'
plot,MgsaResults: no visible global function definition for
'close.screen'
Undefined global functions or variables:
barplot2 callNextMethod close.screen na.omit new par read.delim
relist screen sd split.screen str
Consider adding
importFrom("graphics", "close.screen", "par", "screen", "split.screen")
importFrom("methods", "callNextMethod", "new")
importFrom("stats", "na.omit", "sd")
importFrom("utils", "read.delim", "relist", "str")
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 ... OK
* checking for code/documentation mismatches ... OK
* 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 shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... NOTE
PKG_CXXFLAGS set in 'src/Makevars.in' without any corresponding files
* 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/mgsa/libs/i386/mgsa.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/mgsa/libs/x64/mgsa.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'printf', possibly from 'printf' (C)
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
readGAF 5.88 0.75 6.64
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
readGAF 5.64 0.85 6.48
* 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: 6 NOTEs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/mgsa.Rcheck/00check.log'
for details.
mgsa.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/mgsa_1.40.0.tar.gz && rm -rf mgsa.buildbin-libdir && mkdir mgsa.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=mgsa.buildbin-libdir mgsa_1.40.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL mgsa_1.40.0.zip && rm mgsa_1.40.0.tar.gz mgsa_1.40.0.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 216k 100 216k 0 0 954k 0 --:--:-- --:--:-- --:--:-- 959k
install for i386
* installing *source* package 'mgsa' ...
** using staged installation
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** 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 mgsa-core.c -o mgsa-core.o
mgsa-core.c: In function 'ts_R_alloc':
mgsa-core.c:56: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
#pragma omp critical
"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 mgsa.c -o mgsa.o
mgsa.c: In function 'mgsa_mcmc':
mgsa.c:552: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
mgsa.c:558: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
#pragma omp critical
"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 mt.c -o mt.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o mgsa.dll tmp.def mgsa-core.o mgsa.o mt.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/mgsa.buildbin-libdir/00LOCK-mgsa/00new/mgsa/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'mgsa'
finding HTML links ... done
MgsaGoSets-class html
MgsaMcmcResults-class html
MgsaResults-class html
MgsaSets-class html
alphaMcmcPost-methods html
alphaPost-methods html
betaMcmcPost-methods html
betaPost-methods html
createMgsaGoSets html
example-go html
example-o html
itemAnnotations-methods html
itemIndices-methods html
length-methods html
mgsa-methods html
mgsa-package html
nsamples-methods html
pMcmcPost-methods html
pPost-methods html
plot-MgsaResults-method html
populationSize-methods html
readGAF html
restarts-methods html
setAnnotations-methods html
setsMcmcPost-methods html
setsResults-methods html
show-MgsaResults-method html
show-MgsaSets-method html
steps-methods html
studySetSizeInPopulation-methods html
subMgsaSets-methods 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 'mgsa' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** 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 mgsa-core.c -o mgsa-core.o
mgsa-core.c: In function 'ts_R_alloc':
mgsa-core.c:56: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
#pragma omp critical
"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 mgsa.c -o mgsa.o
mgsa.c: In function 'mgsa_mcmc':
mgsa.c:552: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
mgsa.c:558: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
#pragma omp critical
"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 mt.c -o mt.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o mgsa.dll tmp.def mgsa-core.o mgsa.o mt.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/mgsa.buildbin-libdir/mgsa/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mgsa' as mgsa_1.40.0.zip
* DONE (mgsa)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'mgsa' successfully unpacked and MD5 sums checked
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mgsa.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("mgsa")
Loading required package: gplots
Attaching package: 'gplots'
The following object is masked from 'package:stats':
lowess
>
>
> test_check("mgsa")
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 19 ]
>
> proc.time()
user system elapsed
8.90 0.68 9.56
|
mgsa.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("mgsa")
Loading required package: gplots
Attaching package: 'gplots'
The following object is masked from 'package:stats':
lowess
>
>
> test_check("mgsa")
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 19 ]
>
> proc.time()
user system elapsed
9.34 0.81 10.18
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mgsa.Rcheck/examples_i386/mgsa-Ex.timings
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mgsa.Rcheck/examples_x64/mgsa-Ex.timings
|