Karl J. Dykema
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/reb |
| Branch: RELEASE_3_9 |
| Last Commit: e645a67 |
| Last Changed Date: 2019-05-02 11:53:04 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:20:11 -0400 (Wed, 16 Oct 2019).
| Package 1343/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| reb 1.62.0 Karl J. Dykema
| 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: reb |
| Version: 1.62.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:reb.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings reb_1.62.0.tar.gz |
| StartedAt: 2019-10-16 06:24:50 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 06:27:23 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 153.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: reb.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:reb.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings reb_1.62.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/reb.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'reb/DESCRIPTION' ... OK
* this is package 'reb' version '1.62.0'
* 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 'reb' 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
Missing object imported by a ':::' call: 'Biobase:::EXPRSET_DEPR_MSG'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.MAP2chromLoc: warning in mget(subnames, env = chrEnv, ifnotfound =
NA): partial argument match of 'env' to 'envir'
rmAmbigMappings: warning in ls(env = get(package)): partial argument
match of 'env' to 'envir'
.genMeanMatrix: no visible global function definition for 't.test'
buildChromCytoband: no visible global function definition for 'new'
buildChromCytoband: no visible binding for global variable
'Hs.cytoband'
buildChromCytoband: no visible binding for global variable
'Rn.cytoband'
buildChromCytoband: no visible binding for global variable
'Mm.cytoband'
buildChromMap: no visible global function definition for 'new'
cgma: no visible binding for global variable 't.test'
cset2band: no visible global function definition for 'aggregate'
fromRevIsh: no visible binding for global variable 'vai.chr'
reb: no visible global function definition for 'supsmu'
reb: no visible global function definition for 'lowess'
reb: no visible global function definition for 'approx'
regmap: no visible global function definition for 'par'
regmap: no visible global function definition for 'layout'
regmap: no visible global function definition for 'image'
regmap: no visible global function definition for 'axis'
smoothByRegion: no visible global function definition for 'supsmu'
smoothByRegion: no visible global function definition for 'lowess'
smoothByRegion: no visible global function definition for 'approx'
summarizeByRegion: no visible binding for global variable 't.test'
tBinomTest: no visible global function definition for 'binom.test'
writeGFF3: no visible global function definition for 'write.table'
Undefined global functions or variables:
Hs.cytoband Mm.cytoband Rn.cytoband aggregate approx axis binom.test
image layout lowess new par supsmu t.test vai.chr write.table
Consider adding
importFrom("graphics", "axis", "image", "layout", "par")
importFrom("methods", "new")
importFrom("stats", "aggregate", "approx", "binom.test", "lowess",
"supsmu", "t.test")
importFrom("utils", "write.table")
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 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-3.9-bioc/R/library/reb/libs/i386/reb.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'printf', possibly from 'printf' (C)
Found 'putchar', possibly from 'putchar' (C)
Found 'puts', possibly from 'printf' (C), 'puts' (C)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/reb/libs/x64/reb.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'printf', possibly from 'printf' (C)
Found 'putchar', possibly from 'putchar' (C)
Found 'puts', possibly from 'printf' (C), 'puts' (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
** running examples for arch 'x64' ... 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: 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/reb.Rcheck/00check.log'
for details.
reb.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/reb_1.62.0.tar.gz && rm -rf reb.buildbin-libdir && mkdir reb.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=reb.buildbin-libdir reb_1.62.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL reb_1.62.0.zip && rm reb_1.62.0.tar.gz reb_1.62.0.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 489k 100 489k 0 0 6687k 0 --:--:-- --:--:-- --:--:-- 7422k
install for i386
* installing *source* package 'reb' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c movbin.c -o movbin.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o reb.dll tmp.def movbin.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/reb.buildbin-libdir/00LOCK-reb/00new/reb/libs/i386
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'reb'
finding HTML links ... done
Hs.arms html
absMax html
buildChromCytoband html
buildChromMap html
cset2band html
fromRevIsh html
isAbnormal html
mcr.eset html
movbin html
movt html
naMean html
regmap html
revish html
rmAmbigMappings html
smoothByRegion html
summarizeByRegion html
tBinomTest html
writeGFF3 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 'reb' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c movbin.c -o movbin.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o reb.dll tmp.def movbin.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/reb.buildbin-libdir/reb/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'reb' as reb_1.62.0.zip
* DONE (reb)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'reb' successfully unpacked and MD5 sums checked
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reb.Rcheck/examples_i386/reb-Ex.timings
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reb.Rcheck/examples_x64/reb-Ex.timings
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