Olga Ivanova
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/CARNIVAL |
| git_branch: RELEASE_3_14 |
| git_last_commit: c22da3e |
| git_last_commit_date: 2021-10-26 12:59:23 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:06:17 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the CARNIVAL package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CARNIVAL.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 247/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CARNIVAL 2.4.0 (landing page) Olga Ivanova
| nebbiolo2 | Linux (Ubuntu 20.04.4 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: CARNIVAL |
| Version: 2.4.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CARNIVAL.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings CARNIVAL_2.4.0.tar.gz |
| StartedAt: 2022-04-12 16:50:34 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 16:51:31 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 57.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CARNIVAL.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CARNIVAL.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings CARNIVAL_2.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/CARNIVAL.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CARNIVAL/DESCRIPTION' ... OK
* this is package 'CARNIVAL' version '2.4.0'
* package encoding: UTF-8
* 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 ... NOTE
Found the following hidden files and directories:
.travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'CARNIVAL' 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 ... 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
Namespaces in Imports field not imported from:
'methods' 'rmarkdown'
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
convergenceTextToTable: no visible binding for global variable '.'
convergenceTextToTable: no visible binding for global variable 'Gap'
convergenceTextToTable: no visible global function definition for
'across'
convergenceTextToTable: no visible global function definition for
'everything'
convergenceTextToTable: no visible binding for global variable
'Objective'
convergenceTextToTable: no visible binding for global variable 'Best
Bound'
convergenceTextToTable: no visible global function definition for 'n'
convergenceTextToTable: no visible binding for global variable 'index'
defaultCbcSolveCarnivalOptions: no visible binding for global variable
'solverPath'
exportIlpSolutionResultFromXml: no visible global function definition
for 'is'
parseCplexLog: no visible binding for global variable '.'
prepareLPMatrixSingle: no visible global function definition for
'error'
solveWithCbc: no visible global function definition for 'read.csv2'
solveWithCplex: no visible global function definition for 'read.delim'
timeStringToTable: no visible binding for global variable '.'
timeStringToTable: no visible binding for global variable 'ticks'
timeStringToTable: no visible binding for global variable 'Solutions'
timeStringToTable: no visible global function definition for 'across'
timeStringToTable: no visible global function definition for
'everything'
writeCplexCommandFileFromJson: no visible global function definition
for 'fromJSON'
Undefined global functions or variables:
. Best Bound Gap Objective Solutions across error everything fromJSON
index is n read.csv2 read.delim solverPath ticks
Consider adding
importFrom("methods", "is")
importFrom("utils", "read.csv2", "read.delim")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
prepare_Rd: checkData.Rd:23-25: Dropping empty section \value
prepare_Rd: checkOptionsValidity.Rd:14-16: Dropping empty section \value
prepare_Rd: defaultCbcSolveCarnivalOptions.Rd:12-14: Dropping empty section \value
prepare_Rd: defaultCplexSpecificOptions.Rd:12-14: Dropping empty section \value
prepare_Rd: defaultLpSolveCarnivalOptions.Rd:12-14: Dropping empty section \value
prepare_Rd: setCarnivalOptions.Rd:14-16: Dropping empty section \value
prepare_Rd: solveWithCbc.Rd:12-14: Dropping empty section \value
prepare_Rd: suggestedCbcSpecificOptions.Rd:12-14: Dropping empty section \value
prepare_Rd: suggestedCplexSpecificOptions.Rd:12-14: Dropping empty section \value
* 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 R/sysdata.rda ... 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-3.14-bioc/meat/CARNIVAL.Rcheck/00check.log'
for details.
CARNIVAL.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/CARNIVAL_2.4.0.tar.gz && rm -rf CARNIVAL.buildbin-libdir && mkdir CARNIVAL.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CARNIVAL.buildbin-libdir CARNIVAL_2.4.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL CARNIVAL_2.4.0.zip && rm CARNIVAL_2.4.0.tar.gz CARNIVAL_2.4.0.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 2494k 3 98k 0 0 436k 0 0:00:05 --:--:-- 0:00:05 437k
54 2494k 54 1353k 0 0 1104k 0 0:00:02 0:00:01 0:00:01 1105k
100 2494k 100 2494k 0 0 1373k 0 0:00:01 0:00:01 --:--:-- 1373k
install for i386
* installing *source* package 'CARNIVAL' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'CARNIVAL'
finding HTML links ... done
addPerturbationNodes html
checkCarnivalOptions html
checkData html
checkOptionsValidity html
checkPriorKnowledgeNetwork html
createInternalDataRepresentation html
defaultCbcSolveCarnivalOptions html
defaultCplexCarnivalOptions html
defaultCplexSpecificOptions html
defaultLpSolveCarnivalOptions html
generateLpFileCarnival html
getOptionsList html
getSupportedSolvers html
getSupportedSolversFunctions html
isInputValidCarnival html
parseCplexLog html
prepareForCarnivalRun html
preprocessPriorKnowledgeNetwork html
processSolution html
readOptions html
runCARNIVAL html
runFromLpCarnival html
runInverseCarnival html
runVanillaCarnival html
sendTaskToSolver html
setCarnivalOptions html
solveCarnival html
solveCarnivalFromLp html
solveWithCbc html
suggestedCbcSpecificOptions html
suggestedCplexSpecificOptions html
writeParsedData 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 'CARNIVAL' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CARNIVAL' as CARNIVAL_2.4.0.zip
* DONE (CARNIVAL)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'CARNIVAL' successfully unpacked and MD5 sums checked
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CARNIVAL.Rcheck/examples_i386/CARNIVAL-Ex.timings
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CARNIVAL.Rcheck/examples_x64/CARNIVAL-Ex.timings
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