Pierrick Roger
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/biodb |
| git_branch: RELEASE_3_13 |
| git_last_commit: 84b7aff |
| git_last_commit_date: 2021-06-09 04:23:12 -0400 (Wed, 09 Jun 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:05:58 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the biodb package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodb.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 178/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodb 1.0.4 (landing page) Pierrick Roger
| 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: biodb |
| Version: 1.0.4 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biodb.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings biodb_1.0.4.tar.gz |
| StartedAt: 2021-10-14 20:14:07 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 20:24:07 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 600.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biodb.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:biodb.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings biodb_1.0.4.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/biodb.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 'biodb/DESCRIPTION' ... OK
* this is package 'biodb' version '1.0.4'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'biodb' can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.1Mb
sub-directories of 1Mb or more:
R 1.7Mb
libs 2.7Mb
* 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 ... OK
* 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 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/biodb/libs/i386/biodb.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/biodb/libs/x64/biodb.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (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 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/biodb.Rcheck/00check.log'
for details.
biodb.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/biodb_1.0.4.tar.gz && rm -rf biodb.buildbin-libdir && mkdir biodb.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=biodb.buildbin-libdir biodb_1.0.4.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL biodb_1.0.4.zip && rm biodb_1.0.4.tar.gz biodb_1.0.4.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 405k 100 405k 0 0 1199k 0 --:--:-- --:--:-- --:--:-- 1204k
install for i386
* installing *source* package 'biodb' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/testthat/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/testthat/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c closeMatchPpm.cpp -o closeMatchPpm.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/testthat/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c test-100-ms_matching.cpp -o test-100-ms_matching.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/testthat/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c test-runner.cpp -o test-runner.o
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/testthat/include/testthat.h:1,
from test-runner.cpp:7:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/testthat/include/testthat/testthat.h: In function 'std::ostream& Catch::cout()':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/testthat/include/testthat/testthat.h:145:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
}
^
C:/Users/biocbuild/bbs-3.13-bioc/R/library/testthat/include/testthat/testthat.h: In function 'std::ostream& Catch::cerr()':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/testthat/include/testthat/testthat.h:152:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
}
^
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o biodb.dll tmp.def RcppExports.o closeMatchPpm.o test-100-ms_matching.o test-runner.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/biodb.buildbin-libdir/00LOCK-biodb/00new/biodb/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'biodb'
finding HTML links ... done
BiodbCompounddbConn-class html
BiodbConfig-class html
BiodbConn-class html
BiodbConnBase-class html
BiodbConnObserver-class html
BiodbCsvEntry-class html
BiodbDbInfo-class html
BiodbDbsInfo-class html
BiodbDownloadable-class html
BiodbEditable-class html
BiodbEntry-class html
BiodbEntryField-class html
BiodbEntryFields-class html
BiodbFactory-class html
BiodbHtmlEntry-class html
BiodbJsonEntry-class html
BiodbListEntry-class html
BiodbMain-class html
BiodbMassdbConn-class html
BiodbObserver-class html
BiodbPersistentCache-class html
BiodbRemotedbConn-class html
BiodbRequest html
BiodbRequestScheduler-class html
BiodbRequestSchedulerRule html
BiodbSdfEntry-class html
BiodbSqlBinaryOp html
BiodbSqlExpr html
BiodbSqlField html
BiodbSqlList html
BiodbSqlLogicalOp html
BiodbSqlQuery html
BiodbSqlValue html
BiodbTestMsgAck-class html
BiodbTxtEntry-class html
BiodbUrl html
BiodbWritable-class html
BiodbXmlEntry-class html
CompCsvFileConn-class html
CompCsvFileEntry-class html
CompSqliteConn-class html
CompSqliteEntry-class html
CsvFileConn-class html
ExtConnClass html
ExtCpp html
ExtDefinitions html
ExtDescriptionFile html
ExtEntryClass html
ExtFileGenerator html
ExtGenerator html
ExtGitignore html
ExtLicense html
ExtMakefile html
ExtPackage html
ExtPackageFile html
ExtRbuildignore html
ExtReadme html
ExtTests html
ExtTravisFile html
ExtVignette html
FileTemplate html
MassCsvFileConn-class html
MassCsvFileEntry-class html
MassSqliteConn-class html
MassSqliteEntry-class html
Progress html
Range html
SqliteConn-class html
biodb-package html
closeMatchPpm html
connNameToClassPrefix html
createBiodbTestInstance html
df2str html
error html
error0 html
genNewExtPkg html
getConnClassName html
getConnTypes html
getEntryClassName html
getEntryTypes html
getLicenses html
getLogger html
getPkgName html
getReposName html
getTestOutputDir html
listTestRefEntries html
logDebug html
logDebug0 html
logInfo html
logInfo0 html
logTrace html
logTrace0 html
lst2str html
newInst html
runGenericTests html
testContext html
testThat html
upgradeExtPkg html
warn html
warn0 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 'biodb' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/testthat/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/testthat/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c closeMatchPpm.cpp -o closeMatchPpm.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/testthat/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c test-100-ms_matching.cpp -o test-100-ms_matching.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/testthat/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c test-runner.cpp -o test-runner.o
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/testthat/include/testthat.h:1,
from test-runner.cpp:7:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/testthat/include/testthat/testthat.h: In function 'std::ostream& Catch::cout()':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/testthat/include/testthat/testthat.h:145:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
}
^
C:/Users/biocbuild/bbs-3.13-bioc/R/library/testthat/include/testthat/testthat.h: In function 'std::ostream& Catch::cerr()':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/testthat/include/testthat/testthat.h:152:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
}
^
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o biodb.dll tmp.def RcppExports.o closeMatchPpm.o test-100-ms_matching.o test-runner.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/biodb.buildbin-libdir/biodb/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'biodb' as biodb_1.0.4.zip
* DONE (biodb)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'biodb' successfully unpacked and MD5 sums checked
|
biodb.Rcheck/tests_i386/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodb)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> test_check("biodb")
[ FAIL 0 | WARN 19 | SKIP 0 | PASS 1386 ]
>
> proc.time()
user system elapsed
148.45 9.95 160.39
|
biodb.Rcheck/tests_x64/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodb)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> test_check("biodb")
[ FAIL 0 | WARN 19 | SKIP 0 | PASS 1386 ]
>
> proc.time()
user system elapsed
188.92 11.29 248.29
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biodb.Rcheck/examples_i386/biodb-Ex.timings
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biodb.Rcheck/examples_x64/biodb-Ex.timings
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