Justin Lee
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/CGEN |
| git_branch: master |
| git_last_commit: 72494d0 |
| git_last_commit_date: 2021-10-26 13:08:59 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:09 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 CGEN package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CGEN.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 283/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CGEN 3.31.0 (landing page) Justin Lee
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | ERROR | ERROR | skipped | skipped | |||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: CGEN |
| Version: 3.31.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CGEN.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings CGEN_3.31.0.tar.gz |
| StartedAt: 2022-03-17 18:41:55 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:44:38 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 163.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CGEN.Rcheck |
| Warnings: 0 |
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CGEN.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings CGEN_3.31.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/CGEN.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CGEN/DESCRIPTION' ... OK
* this is package 'CGEN' version '3.31.0'
* 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 'CGEN' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
GPL-2 + file LICENSE
* 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
* 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 x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/CGEN/libs/x64/CGEN.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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
additive.test 61.14 4.00 65.14
getMatchedSets 7.11 0.77 7.88
snp.matched 7.09 0.03 7.12
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/CGEN.Rcheck/00check.log'
for details.
CGEN.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL CGEN
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'CGEN' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c Additive.c -o Additive.o
Additive.c: In function 'compute_g':
Additive.c:233:19: warning: 'et22' may be used uninitialized in this function [-Wmaybe-uninitialized]
x = et12 + et22 - 1;
~~~~~^~~~~~
Additive.c:235:25: warning: 't22' may be used uninitialized in this function [-Wmaybe-uninitialized]
*g22 = logx - t12 - t22;
~~~~~~~~~~~^~~~~
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c CML.c -o CML.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ccl.c -o ccl.o
"C:/rtools40/mingw64/bin/"gfortran -fno-optimize-sibling-calls -O2 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c csclust.f -o csclust.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c fsclust.c -o fsclust.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c hcl.c -o hcl.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pmatch.c -o pmatch.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c score.c -o score.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o CGEN.dll tmp.def Additive.o CML.o ccl.o csclust.o fsclust.o hcl.o pmatch.o score.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -lgfortran -lm -lquadmath -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-CGEN/00new/CGEN/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'CGEN'
finding HTML links ... done
CGEN html
GxE.scan html
GxE.scan.combine html
GxE.scan.partition html
LocusMapData html
QQ.plot html
Xdata html
Xdata2 html
additive.test html
chromosome.plot html
getMatchedSets html
getSummary html
getWaldTest html
locusMap.list html
pheno.list html
printEffects html
snp.effects html
snp.effects.plot html
snp.list html
snp.logistic html
snp.matched html
snp.score html
subject.list 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
* DONE (CGEN)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'Travel' is missing or broken
done
CGEN.Rcheck/CGEN-Ex.timings
| name | user | system | elapsed | |
| GxE.scan | 0.00 | 0.01 | 0.02 | |
| GxE.scan.combine | 0 | 0 | 0 | |
| GxE.scan.partition | 0 | 0 | 0 | |
| LocusMapData | 0.00 | 0.03 | 0.03 | |
| QQ.plot | 0.01 | 0.00 | 0.02 | |
| Xdata | 0 | 0 | 0 | |
| Xdata2 | 0.03 | 0.00 | 0.03 | |
| additive.test | 61.14 | 4.00 | 65.14 | |
| chromosome.plot | 0.36 | 0.00 | 0.36 | |
| getMatchedSets | 7.11 | 0.77 | 7.88 | |
| getSummary | 0 | 0 | 0 | |
| getWaldTest | 0.02 | 0.00 | 0.01 | |
| printEffects | 0.25 | 0.02 | 0.27 | |
| snp.effects | 0.22 | 0.00 | 0.22 | |
| snp.effects.plot | 0.73 | 0.00 | 0.73 | |
| snp.list | 0 | 0 | 0 | |
| snp.logistic | 0.55 | 0.00 | 0.55 | |
| snp.matched | 7.09 | 0.03 | 7.12 | |
| snp.score | 0.03 | 0.00 | 0.03 | |