Robin Andersson
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/SMAP |
| git_branch: RELEASE_3_13 |
| git_last_commit: c2fb485 |
| git_last_commit_date: 2021-05-19 11:39:26 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:23 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the SMAP package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SMAP.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 1793/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SMAP 1.56.0 (landing page) Robin Andersson
| 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: SMAP |
| Version: 1.56.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SMAP.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings SMAP_1.56.0.tar.gz |
| StartedAt: 2021-10-15 05:53:51 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 05:55:04 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 73.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SMAP.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:SMAP.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings SMAP_1.56.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/SMAP.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 'SMAP/DESCRIPTION' ... OK
* this is package 'SMAP' version '1.56.0'
* 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 'SMAP' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
'library' or 'require' call to 'methods' which was already attached by Depends.
Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File 'SMAP/R/AllClasses.R':
.onLoad calls:
require("methods", quietly = TRUE)
Package startup functions should not change the search path.
See section 'Good practice' in '?.onAttach'.
.draw.dist,gaussparam: no visible global function definition for
'abline'
plot,SMAPObservations-missing: no visible global function definition
for 'par'
plot,SMAPObservations-missing: no visible global function definition
for 'points'
plot,SMAPObservations-missing: no visible global function definition
for 'abline'
plot,SMAPObservations-missing: no visible global function definition
for 'box'
plot,SMAPObservations-missing: no visible global function definition
for 'axis'
profilePlot,SMAPProfile: no visible global function definition for
'par'
profilePlot,SMAPProfile: no visible global function definition for
'points'
profilePlot,SMAPProfile: no visible global function definition for
'abline'
profilePlot,SMAPProfile: no visible global function definition for
'box'
profilePlot,SMAPProfile: no visible global function definition for
'axis'
profilePlot,SMAPProfiles: no visible global function definition for
'par'
profilePlot,SMAPProfiles: no visible global function definition for
'abline'
profilePlot,SMAPProfiles: no visible global function definition for
'box'
profilePlot,SMAPProfiles: no visible global function definition for
'axis'
Undefined global functions or variables:
abline axis box par points
Consider adding
importFrom("graphics", "abline", "axis", "box", "par", "points")
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 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-3.13-bioc/R/library/SMAP/libs/i386/SMAP.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/SMAP/libs/x64/SMAP.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
smap 11.81 0.03 11.86
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
smap 11.23 0.04 11.28
* 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: 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/SMAP.Rcheck/00check.log'
for details.
SMAP.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/SMAP_1.56.0.tar.gz && rm -rf SMAP.buildbin-libdir && mkdir SMAP.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SMAP.buildbin-libdir SMAP_1.56.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL SMAP_1.56.0.zip && rm SMAP_1.56.0.tar.gz SMAP_1.56.0.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
3 506k 3 15989 0 0 135k 0 0:00:03 --:--:-- 0:00:03 135k
100 506k 100 506k 0 0 1684k 0 --:--:-- --:--:-- --:--:-- 1682k
install for i386
* installing *source* package 'SMAP' ...
** 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 gradient.c -o gradient.o
gradient.c: In function 'prior_gradient':
gradient.c:142:7: warning: variable 'lower' set but not used [-Wunused-but-set-variable]
int lower;
^~~~~
gradient.c: In function 'hmm_update':
gradient.c:247:10: warning: unused variable 'tmp' [-Wunused-variable]
double tmp;
^~~
"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 init.c -o init.o
"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 overlap.c -o overlap.o
"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 prob.c -o prob.o
"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 viterbi.c -o viterbi.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o SMAP.dll tmp.def gradient.o init.o overlap.o prob.o viterbi.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/SMAP.buildbin-libdir/00LOCK-SMAP/00new/SMAP/libs/i386
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'SMAP'
finding HTML links ... done
GBM html
SMAP-internal html
SMAPHMM-class html
SMAPHMM html
SMAPObservations-class html
SMAPObservations html
SMAPProfile-class html
SMAPProfiles-class html
smap 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 'SMAP' ...
** 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 gradient.c -o gradient.o
gradient.c: In function 'prior_gradient':
gradient.c:142:7: warning: variable 'lower' set but not used [-Wunused-but-set-variable]
int lower;
^~~~~
gradient.c: In function 'hmm_update':
gradient.c:247:10: warning: unused variable 'tmp' [-Wunused-variable]
double tmp;
^~~
"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 init.c -o init.o
"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 overlap.c -o overlap.o
"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 prob.c -o prob.o
"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 viterbi.c -o viterbi.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o SMAP.dll tmp.def gradient.o init.o overlap.o prob.o viterbi.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/SMAP.buildbin-libdir/SMAP/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SMAP' as SMAP_1.56.0.zip
* DONE (SMAP)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'SMAP' successfully unpacked and MD5 sums checked
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SMAP.Rcheck/examples_i386/SMAP-Ex.timings
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SMAP.Rcheck/examples_x64/SMAP-Ex.timings
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