Ivana Ihnatova
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/ToPASeq |
| Branch: RELEASE_3_11 |
| Last Commit: 41cc282 |
| Last Changed Date: 2020-04-27 14:44:57 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:57:56 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE ToPASeq PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1813/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ToPASeq 1.22.0 Ivana Ihnatova
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | NA | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |
| Package: ToPASeq |
| Version: 1.22.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ToPASeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings ToPASeq_1.22.0.tar.gz |
| StartedAt: 2020-10-17 08:54:05 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 08:59:39 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 333.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ToPASeq.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ToPASeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings ToPASeq_1.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/ToPASeq.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 'ToPASeq/DESCRIPTION' ... OK
* this is package 'ToPASeq' version '1.22.0'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'ToPASeq' 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 ... NOTE
drawGraph: no visible global function definition for 'renderGraph'
estimateCF: no visible global function definition for 'buildGraphNEL'
makeLegend: no visible global function definition for 'image'
makeLegend: no visible global function definition for 'axis'
makeLegend: no visible global function definition for 'mtext'
makeNodeSizeLegend: no visible global function definition for
'layoutGraph'
makeNodeSizeLegend: no visible global function definition for
'renderGraph'
plot.topResult: no visible global function definition for 'reduceGraph'
plotCliques: no visible global function definition for 'layoutGraph'
plotRagraph : .local: no visible binding for global variable
'drawAgNode'
plotRagraph : .local: no visible global function definition for
'graphLayout'
plotRagraph : .local: no visible global function definition for
'upRight'
plotRagraph : .local: no visible global function definition for
'boundBox'
plotRagraph : .local: no visible global function definition for
'botLeft'
plotRagraph : .local: no visible global function definition for 'getX'
plotRagraph : .local: no visible global function definition for 'getY'
plotRagraph : .local: no visible global function definition for
'AgNode'
plotRagraph : .local: no visible global function definition for
'getNodeRW'
plotRagraph : .local : <anonymous>: no visible global function
definition for 'getNodeRW'
plotRagraph : .local : <anonymous>: no visible global function
definition for 'getNodeLW'
plotRagraph : .local : <anonymous>: no visible global function
definition for 'getNodeHeight'
plotRagraph : .local : <anonymous>: no visible global function
definition for 'labelText'
plotRagraph : .local : <anonymous>: no visible global function
definition for 'txtLabel'
plotRagraph : .local: no visible global function definition for
'AgEdge'
renderOrig: no visible global function definition for 'layoutGraph'
renderReduced: no visible global function definition for 'reduceGraph'
renderReduced: no visible global function definition for 'layoutGraph'
renderSpline: no visible global function definition for 'bezierPoints'
shadowtext: no visible global function definition for 'xy.coords'
shadowtext: no visible global function definition for 'grconvertX'
shadowtext: no visible global function definition for 'grconvertY'
Undefined global functions or variables:
AgEdge AgNode axis bezierPoints botLeft boundBox buildGraphNEL
drawAgNode getNodeHeight getNodeLW getNodeRW getX getY graphLayout
grconvertX grconvertY image labelText layoutGraph mtext reduceGraph
renderGraph txtLabel upRight xy.coords
Consider adding
importFrom("grDevices", "xy.coords")
importFrom("graphics", "axis", "grconvertX", "grconvertY", "image",
"mtext")
to your NAMESPACE file.
* 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 ... WARNING
Documented arguments not in \usage in documentation object 'res':
'...'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... 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/ToPASeq/libs/i386/ToPASeq.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/ToPASeq/libs/x64/ToPASeq.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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
CePa 7.42 0.81 10.02
TAPPA 7.54 0.21 7.73
PRS 6.01 0.08 6.14
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
TAPPA 8.11 0.21 8.33
CePa 5.57 0.19 5.77
* 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: 1 WARNING, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/ToPASeq.Rcheck/00check.log'
for details.
ToPASeq.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/ToPASeq_1.22.0.tar.gz && rm -rf ToPASeq.buildbin-libdir && mkdir ToPASeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ToPASeq.buildbin-libdir ToPASeq_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL ToPASeq_1.22.0.zip && rm ToPASeq_1.22.0.tar.gz ToPASeq_1.22.0.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 60666 100 60666 0 0 926k 0 --:--:-- --:--:-- --:--:-- 1039k
install for i386
* installing *source* package 'ToPASeq' ...
** 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 accCpp.cpp -o accCpp.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 betweeness.cpp -o betweeness.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 colMinMax.cpp -o colMinMax.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 downstream.cpp -o downstream.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o ToPASeq.dll tmp.def RcppExports.o accCpp.o betweeness.o colMinMax.o downstream.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/ToPASeq.buildbin-libdir/00LOCK-ToPASeq/00new/ToPASeq/libs/i386
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'ToPASeq'
finding HTML links ... done
CePa html
DEGraph html
PRS html
finding level-2 HTML links ... done
PRS_wrapper html
PWEA html
SPIA html
TAPPA html
TopologyGSA html
clipper html
convertIdentifiersByVector html
res 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 'ToPASeq' ...
** 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 accCpp.cpp -o accCpp.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 betweeness.cpp -o betweeness.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 colMinMax.cpp -o colMinMax.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 downstream.cpp -o downstream.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o ToPASeq.dll tmp.def RcppExports.o accCpp.o betweeness.o colMinMax.o downstream.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/ToPASeq.buildbin-libdir/ToPASeq/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ToPASeq' as ToPASeq_1.22.0.zip
* DONE (ToPASeq)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'ToPASeq' successfully unpacked and MD5 sums checked
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ToPASeq.Rcheck/examples_i386/ToPASeq-Ex.timings
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ToPASeq.Rcheck/examples_x64/ToPASeq-Ex.timings
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