Christopher Bare
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/gaggle |
| Branch: RELEASE_3_9 |
| Last Commit: 71123ad |
| Last Changed Date: 2019-05-02 11:53:06 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:20:40 -0400 (Wed, 16 Oct 2019).
| Package 601/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| gaggle 1.52.0 Christopher Bare
| 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: gaggle |
| Version: 1.52.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gaggle.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings gaggle_1.52.0.tar.gz |
| StartedAt: 2019-10-16 03:49:06 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 03:51:10 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 123.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: gaggle.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:gaggle.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings gaggle_1.52.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/gaggle.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 'gaggle/DESCRIPTION' ... OK
* this is package 'gaggle' version '1.52.0'
* 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 'gaggle' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Non-standard license specification:
GPL version 2 or newer
Standardizable: TRUE
Standardized license specification:
GPL (>= 2)
* 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' calls to packages already attached by Depends:
'RUnit' 'rJava'
Please remove these calls from your code.
Packages in Depends field not imported from:
'RUnit' 'rJava'
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
File 'gaggle/R/gaggle.R':
.onLoad calls:
require("rJava")
cat(paste("\nonLoad -- libname:", libname, "pkgname:", pkgname, "\n"))
cat("path to jar:", fullPathToGaggleJar, "\n")
cat(" script: ", .scriptVersion(), "\n")
cat(" os version: ", .jcall("java/lang/System", "S", "getProperty", "os.name"), "\n")
cat(" jvm version: ", jvmVersion, "\n")
cat("\n You are using the wrong version of Java.\n", " Please see http://gaggle.systemsbiology.org/docs/html/java\n\n")
Package startup functions should not change the search path.
Package startup functions should use 'packageStartupMessage' to
generate messages.
See section 'Good practice' in '?.onAttach'.
onLoad -- libname: C:/Users/biocbuild/bbs-3.9-bioc/R/library pkgname: gaggle
path to jar: C:/Users/biocbuild/bbs-3.9-bioc/R/library/gaggle/jars/gaggleRShell.jar
script: gaggle.R $Revision: 4499 $ $Date: 2010-08-10 17:15:03 -0700 (Tue, 10 Aug 2010) $
os version: Windows Server 2012 R2
jvm version: 1.8.0_111
You are using the wrong version of Java.
Please see http://gaggle.systemsbiology.org/docs/html/java
.broadcastAssociativeArray: no visible binding for global variable
'goose'
.broadcastEnvironment: no visible binding for global variable 'goose'
.broadcastGraph: no visible binding for global variable 'goose'
.pkgVersion: no visible global function definition for 'sessionInfo'
broadcast: no visible binding for global variable 'goose'
connectToGaggle: no visible binding for global variable 'goose'
disconnectFromGaggle: no visible binding for global variable 'goose'
gaggleInit: no visible binding for '<<-' assignment to 'goose'
gaggleInit: no visible binding for '<<-' assignment to 'targetGoose'
gaggleInit: no visible binding for global variable 'goose'
geese: no visible binding for global variable 'goose'
getCluster: no visible binding for global variable 'goose'
getMatrix: no visible binding for global variable 'goose'
getNameList: no visible binding for global variable 'goose'
getNetwork: no visible binding for global variable 'goose'
getSpecies: no visible binding for global variable 'goose'
getTargetGoose: no visible binding for global variable 'goose'
getTuple: no visible binding for global variable 'goose'
getTupleAsList: no visible binding for global variable 'goose'
hideGoose: no visible binding for global variable 'goose'
setSpecies: no visible binding for global variable 'goose'
setTargetGoose: no visible binding for '<<-' assignment to
'targetGoose'
setTargetGoose: no visible binding for global variable 'goose'
showGoose: no visible binding for global variable 'goose'
testGagglePackage: no visible global function definition for
'test.gaggle'
Undefined global functions or variables:
goose sessionInfo test.gaggle
Consider adding
importFrom("utils", "sessionInfo")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: connectToGaggle.Rd:9-10: Dropping empty section \arguments
prepare_Rd: disconnectFromGaggle.Rd:8-9: Dropping empty section \arguments
prepare_Rd: getCluster.Rd:8-9: Dropping empty section \arguments
prepare_Rd: getNameList.Rd:8-9: Dropping empty section \arguments
prepare_Rd: getTuple.Rd:6-7: Dropping empty section \arguments
* 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 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/gaggle.Rcheck/00check.log'
for details.
gaggle.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/gaggle_1.52.0.tar.gz && rm -rf gaggle.buildbin-libdir && mkdir gaggle.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=gaggle.buildbin-libdir gaggle_1.52.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL gaggle_1.52.0.zip && rm gaggle_1.52.0.tar.gz gaggle_1.52.0.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 184k 100 184k 0 0 3033k 0 --:--:-- --:--:-- --:--:-- 3424k
install for i386
* installing *source* package 'gaggle' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'gaggle'
finding HTML links ... done
broadcast html
connectToGaggle html
disconnectFromGaggle html
gaggleInit html
geese html
getCluster html
getJavaClassName html
getMatrix html
getNameList html
getNetwork html
getSpecies html
getTargetGoose html
getTuple html
hideGoose html
newTuple html
setSpecies html
setTargetGoose html
showGoose html
testGagglePackage html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
onLoad -- libname: C:/Users/biocbuild/bbs-3.9-bioc/meat/gaggle.buildbin-libdir/00LOCK-gaggle/00new pkgname: gaggle
path to jar: C:/Users/biocbuild/bbs-3.9-bioc/meat/gaggle.buildbin-libdir/00LOCK-gaggle/00new/gaggle/jars/gaggleRShell.jar
script: gaggle.R $Revision: 4499 $ $Date: 2010-08-10 17:15:03 -0700 (Tue, 10 Aug 2010) $
os version: Windows Server 2012 R2
jvm version: 1.8.0_111
You are using the wrong version of Java.
Please see http://gaggle.systemsbiology.org/docs/html/java
** testing if installed package can be loaded from final location
onLoad -- libname: C:/Users/biocbuild/bbs-3.9-bioc/meat/gaggle.buildbin-libdir pkgname: gaggle
path to jar: C:/Users/biocbuild/bbs-3.9-bioc/meat/gaggle.buildbin-libdir/gaggle/jars/gaggleRShell.jar
script: gaggle.R $Revision: 4499 $ $Date: 2010-08-10 17:15:03 -0700 (Tue, 10 Aug 2010) $
os version: Windows Server 2012 R2
jvm version: 1.8.0_111
You are using the wrong version of Java.
Please see http://gaggle.systemsbiology.org/docs/html/java
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'gaggle' ...
** testing if installed package can be loaded
onLoad -- libname: C:/Users/biocbuild/bbs-3.9-bioc/meat/gaggle.buildbin-libdir pkgname: gaggle
path to jar: C:/Users/biocbuild/bbs-3.9-bioc/meat/gaggle.buildbin-libdir/gaggle/jars/gaggleRShell.jar
script: gaggle.R $Revision: 4499 $ $Date: 2010-08-10 17:15:03 -0700 (Tue, 10 Aug 2010) $
os version: Windows Server 2012 R2
jvm version: 1.8.0_111
You are using the wrong version of Java.
Please see http://gaggle.systemsbiology.org/docs/html/java
* MD5 sums
packaged installation of 'gaggle' as gaggle_1.52.0.zip
* DONE (gaggle)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'gaggle' successfully unpacked and MD5 sums checked
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gaggle.Rcheck/examples_i386/gaggle-Ex.timings
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gaggle.Rcheck/examples_x64/gaggle-Ex.timings
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