Soroor Hediyeh zadeh
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/oppar |
| Branch: RELEASE_3_11 |
| Last Commit: 6a96428 |
| Last Changed Date: 2020-04-27 14:56:50 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:57:19 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE oppar PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1241/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| oppar 1.16.0 Soroor Hediyeh zadeh
| malbec2 | Linux (Ubuntu 18.04.4 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: oppar |
| Version: 1.16.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:oppar.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings oppar_1.16.0.tar.gz |
| StartedAt: 2020-10-17 06:39:48 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 06:46:31 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 403.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: oppar.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:oppar.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings oppar_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/oppar.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'oppar/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'oppar' version '1.16.0'
* 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 'oppar' can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.6Mb
sub-directories of 1Mb or more:
data 5.1Mb
* 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
compute.gene.density : <anonymous>: no visible global function
definition for 'ecdf'
compute.geneset.es: no visible global function definition for
'txtProgressBar'
compute.geneset.es: no visible global function definition for
'setTxtProgressBar'
ks_test_m: no visible global function definition for
'setTxtProgressBar'
plage: no visible global function definition for 'txtProgressBar'
plage : <anonymous>: no visible global function definition for 'sd'
plage : <anonymous>: no visible global function definition for
'setTxtProgressBar'
plage: no visible global function definition for 'setTxtProgressBar'
ssgsea: no visible global function definition for 'txtProgressBar'
ssgsea : <anonymous>: no visible global function definition for
'setTxtProgressBar'
ssgsea: no visible global function definition for 'setTxtProgressBar'
zscore: no visible global function definition for 'txtProgressBar'
zscore : <anonymous>: no visible global function definition for 'sd'
zscore : <anonymous>: no visible global function definition for
'setTxtProgressBar'
zscore: no visible global function definition for 'setTxtProgressBar'
computeGeneSetsOverlap,list-ExpressionSet : <anonymous>: no visible
global function definition for 'na.omit'
computeGeneSetsOverlap,list-character : <anonymous>: no visible global
function definition for 'na.omit'
gsva,ExpressionSet-GeneSetCollection: no visible binding for global
variable 'sd'
gsva,ExpressionSet-GeneSetCollection : <anonymous>: no visible global
function definition for 'na.omit'
gsva,ExpressionSet-list: no visible binding for global variable 'sd'
gsva,ExpressionSet-list : <anonymous>: no visible global function
definition for 'na.omit'
gsva,matrix-GeneSetCollection: no visible binding for global variable
'sd'
gsva,matrix-GeneSetCollection : <anonymous>: no visible global function
definition for 'na.omit'
gsva,matrix-list: no visible binding for global variable 'sd'
gsva,matrix-list : <anonymous>: no visible global function definition
for 'na.omit'
opa,matrix: no visible global function definition for 'relevel'
opa,matrix : <anonymous>: no visible global function definition for
'mad'
opa,matrix : <anonymous>: no visible global function definition for
'median'
opa,matrix : <anonymous>: no visible binding for global variable
'quantile'
opa,matrix : <anonymous>: no visible global function definition for
'IQR'
show,OPPARList: no visible global function definition for 'head'
Undefined global functions or variables:
IQR ecdf head mad median na.omit quantile relevel sd
setTxtProgressBar txtProgressBar
Consider adding
importFrom("stats", "IQR", "ecdf", "mad", "median", "na.omit",
"quantile", "relevel", "sd")
importFrom("utils", "head", "setTxtProgressBar", "txtProgressBar")
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-3.11-bioc/R/library/oppar/libs/i386/oppar.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/oppar/libs/x64/oppar.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
getSampleOutlier 20.17 0.42 20.61
getSubtypeProbes 19.70 0.25 19.95
opa 18.63 0.28 19.02
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
opa 24.65 0.03 25.91
getSubtypeProbes 23.84 0.03 25.12
getSampleOutlier 21.24 0.14 21.42
* 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: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/oppar.Rcheck/00check.log'
for details.
oppar.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/oppar_1.16.0.tar.gz && rm -rf oppar.buildbin-libdir && mkdir oppar.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=oppar.buildbin-libdir oppar_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL oppar_1.16.0.zip && rm oppar_1.16.0.tar.gz oppar_1.16.0.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 3438k 100 3438k 0 0 20.1M 0 --:--:-- --:--:-- --:--:-- 20.9M
install for i386
* installing *source* package 'oppar' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_oppar.c -o R_init_oppar.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c kernel_estimation.c -o kernel_estimation.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ks_test.c -o ks_test.o
ks_test.c: In function 'ks_sample':
ks_test.c:22:9: warning: unused variable 'mx_value' [-Wunused-variable]
double mx_value = 0.0;
^~~~~~~~
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o oppar.dll tmp.def R_init_oppar.o kernel_estimation.o ks_test.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/oppar.buildbin-libdir/00LOCK-oppar/00new/oppar/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'oppar'
finding HTML links ... done
OPPARList-class html
bcm html
eset html
getSampleOutlier html
getSubtypeProbes html
gsva html
maupin html
opa html
oppar 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 'oppar' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_oppar.c -o R_init_oppar.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c kernel_estimation.c -o kernel_estimation.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ks_test.c -o ks_test.o
ks_test.c: In function 'ks_sample':
ks_test.c:22:9: warning: unused variable 'mx_value' [-Wunused-variable]
double mx_value = 0.0;
^~~~~~~~
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o oppar.dll tmp.def R_init_oppar.o kernel_estimation.o ks_test.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/oppar.buildbin-libdir/oppar/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'oppar' as oppar_1.16.0.zip
* DONE (oppar)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'oppar' successfully unpacked and MD5 sums checked
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oppar.Rcheck/examples_i386/oppar-Ex.timings
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oppar.Rcheck/examples_x64/oppar-Ex.timings
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