| Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-10-17 11:56:11 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE brendaDb PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 202/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| brendaDb 1.2.0 Yi Zhou
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | ERROR | |||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK |
| Package: brendaDb |
| Version: 1.2.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:brendaDb.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings brendaDb_1.2.0.tar.gz |
| StartedAt: 2020-10-17 02:06:41 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 02:23:04 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 983.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: brendaDb.Rcheck |
| Warnings: NA |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:brendaDb.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings brendaDb_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/brendaDb.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 'brendaDb/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'brendaDb' version '1.2.0'
* 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
.github
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 'brendaDb' 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 ... 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 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/brendaDb/libs/i386/brendaDb.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-3.11-bioc/R/library/brendaDb/libs/x64/brendaDb.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' ... ERROR
Running examples in 'brendaDb-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BiocycPathwayEnzymes
> ### Title: Get all EC numbers involved in a BioCyc pathway.
> ### Aliases: BiocycPathwayEnzymes
>
> ### ** Examples
>
> BiocycPathwayEnzymes("HUMAN", "PWY66-400")
Error in close.connection(con) : invalid connection
Calls: BiocycPathwayEnzymes ... tryCatchOne -> <Anonymous> -> close -> close.connection
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'brendaDb-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BiocycPathwayEnzymes
> ### Title: Get all EC numbers involved in a BioCyc pathway.
> ### Aliases: BiocycPathwayEnzymes
>
> ### ** Examples
>
> BiocycPathwayEnzymes("HUMAN", "PWY66-400")
Error in close.connection(con) : invalid connection
Calls: BiocycPathwayEnzymes ... tryCatchOne -> <Anonymous> -> close -> close.connection
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
6. brendaDb::BiocycPathwayGenes(org.id = "HUMAN", pathway = "PWY66666")
7. base::tryCatch(...)
8. base:::tryCatchList(expr, classes, parentenv, handlers)
9. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
10. value[[3L]](cond)
12. base::close.connection(con)
There were 42 warnings (use warnings() to see them)
== testthat results ===========================================================
[ OK: 108 | SKIPPED: 0 | WARNINGS: 113 | FAILED: 2 ]
1. Error: Get enzymes in BioCyc pathway (@test-biocyc.R#6)
2. Error: Get genes in BioCyc pathway (@test-biocyc.R#18)
Error: testthat unit tests failed
Execution halted
** running tests for arch 'x64' ...
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
6. brendaDb::BiocycPathwayGenes(org.id = "HUMAN", pathway = "PWY66666")
7. base::tryCatch(...)
8. base:::tryCatchList(expr, classes, parentenv, handlers)
9. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
10. value[[3L]](cond)
12. base::close.connection(con)
There were 42 warnings (use warnings() to see them)
== testthat results ===========================================================
[ OK: 108 | SKIPPED: 0 | WARNINGS: 113 | FAILED: 2 ]
1. Error: Get enzymes in BioCyc pathway (@test-biocyc.R#6)
2. Error: Get genes in BioCyc pathway (@test-biocyc.R#18)
Error: testthat unit tests failed
Execution halted
* 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 ERRORs, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/brendaDb.Rcheck/00check.log'
for details.
brendaDb.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/brendaDb_1.2.0.tar.gz && rm -rf brendaDb.buildbin-libdir && mkdir brendaDb.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=brendaDb.buildbin-libdir brendaDb_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL brendaDb_1.2.0.zip && rm brendaDb_1.2.0.tar.gz brendaDb_1.2.0.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 364k 100 364k 0 0 1681k 0 --:--:-- --:--:-- --:--:-- 1733k
install for i386
* installing *source* package 'brendaDb' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c read_brenda.cpp -o read_brenda.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o brendaDb.dll tmp.def RcppExports.o read_brenda.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/brendaDb.buildbin-libdir/00LOCK-brendaDb/00new/brendaDb/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'brendaDb'
finding HTML links ... done
BiocycPathwayEnzymes html
BiocycPathwayGenes html
CleanECNumber html
ConfigBPCores html
DownloadBrenda html
ExtractField html
ID2Enzyme html
InitBrendaDeprecatedEntry html
InitBrendaEntry html
ParseGeneric html
ParseNoDescription html
ParseProtein html
ParseProteinNum html
ParseReaction html
ParseRecommendedName html
ParseReference html
ParseSystematicName html
PrettyPrintBrendaEntry html
PrintTreeHelper html
QueryBrenda html
QueryBrendaBase html
ReadBrenda html
ReadBrendaFile html
SelectOrganism html
SeparateEntries html
SeparateSubentries html
ShowFields html
acronyms html
brendaDb-package html
print.brenda.entries html
print.brenda.entry html
*** copying figures
** 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 'brendaDb' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/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-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c read_brenda.cpp -o read_brenda.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o brendaDb.dll tmp.def RcppExports.o read_brenda.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/brendaDb.buildbin-libdir/brendaDb/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'brendaDb' as brendaDb_1.2.0.zip
* DONE (brendaDb)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'brendaDb' successfully unpacked and MD5 sums checked
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brendaDb.Rcheck/tests_i386/testthat.Rout.fail
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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.
> library(testthat)
> library(brendaDb)
>
> test_check("brendaDb")
-- 1. Error: Get enzymes in BioCyc pathway (@test-biocyc.R#6) ----------------
invalid connection
Backtrace:
1. testthat::expect_message(...)
6. brendaDb::BiocycPathwayEnzymes(org.id = "HUMAN", pathway = "PWY66666")
7. base::tryCatch(...)
8. base:::tryCatchList(expr, classes, parentenv, handlers)
9. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
10. value[[3L]](cond)
12. base::close.connection(con)
-- 2. Error: Get genes in BioCyc pathway (@test-biocyc.R#18) -----------------
invalid connection
Backtrace:
1. testthat::expect_message(...)
6. brendaDb::BiocycPathwayGenes(org.id = "HUMAN", pathway = "PWY66666")
7. base::tryCatch(...)
8. base:::tryCatchList(expr, classes, parentenv, handlers)
9. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
10. value[[3L]](cond)
12. base::close.connection(con)
There were 42 warnings (use warnings() to see them)
== testthat results ===========================================================
[ OK: 108 | SKIPPED: 0 | WARNINGS: 113 | FAILED: 2 ]
1. Error: Get enzymes in BioCyc pathway (@test-biocyc.R#6)
2. Error: Get genes in BioCyc pathway (@test-biocyc.R#18)
Error: testthat unit tests failed
Execution halted
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brendaDb.Rcheck/tests_x64/testthat.Rout.fail
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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.
> library(testthat)
> library(brendaDb)
>
> test_check("brendaDb")
-- 1. Error: Get enzymes in BioCyc pathway (@test-biocyc.R#6) ----------------
invalid connection
Backtrace:
1. testthat::expect_message(...)
6. brendaDb::BiocycPathwayEnzymes(org.id = "HUMAN", pathway = "PWY66666")
7. base::tryCatch(...)
8. base:::tryCatchList(expr, classes, parentenv, handlers)
9. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
10. value[[3L]](cond)
12. base::close.connection(con)
-- 2. Error: Get genes in BioCyc pathway (@test-biocyc.R#18) -----------------
invalid connection
Backtrace:
1. testthat::expect_message(...)
6. brendaDb::BiocycPathwayGenes(org.id = "HUMAN", pathway = "PWY66666")
7. base::tryCatch(...)
8. base:::tryCatchList(expr, classes, parentenv, handlers)
9. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
10. value[[3L]](cond)
12. base::close.connection(con)
There were 42 warnings (use warnings() to see them)
== testthat results ===========================================================
[ OK: 108 | SKIPPED: 0 | WARNINGS: 113 | FAILED: 2 ]
1. Error: Get enzymes in BioCyc pathway (@test-biocyc.R#6)
2. Error: Get genes in BioCyc pathway (@test-biocyc.R#18)
Error: testthat unit tests failed
Execution halted
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brendaDb.Rcheck/examples_i386/brendaDb-Ex.timings
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brendaDb.Rcheck/examples_x64/brendaDb-Ex.timings
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