Alex J. Cornish
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/SANTA |
| Branch: RELEASE_3_8 |
| Last Commit: c90410f |
| Last Changed Date: 2018-10-30 11:41:50 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:22:41 -0400 (Sat, 13 Apr 2019).
| Package 1384/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SANTA 2.20.0 Alex J. Cornish
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: SANTA |
| Version: 2.20.0 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SANTA.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings SANTA_2.20.0.tar.gz |
| StartedAt: 2019-04-13 05:17:52 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 05:20:17 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 144.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: SANTA.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SANTA.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings SANTA_2.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/SANTA.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SANTA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SANTA' version '2.20.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 'SANTA' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpakxESn/R.INSTALL1438115c1397/SANTA/man/DistGraph.Rd:53: file link 'shortest.paths' in package 'igraph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpakxESn/R.INSTALL1438115c1397/SANTA/man/GraphDiffusion.Rd:45: file link 'shortest.paths' in package 'igraph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpakxESn/R.INSTALL1438115c1397/SANTA/man/GraphMFPT.Rd:46: file link 'shortest.paths' in package 'igraph' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/SANTA.Rcheck/00install.out' for details.
* 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
Compactness: no visible global function definition for 'pnorm'
Compactness: no visible global function definition for 'sd'
Knet : <anonymous>: no visible global function definition for
'quantile'
Knet: no visible global function definition for 'pnorm'
Knet: no visible global function definition for 'sd'
Knode: no visible global function definition for 'runif'
plot.Knet: no visible global function definition for 'plot'
plot.Knet: no visible global function definition for 'par'
plot.Knet: no visible global function definition for 'polygon'
plot.Knet: no visible global function definition for 'lines'
plot.Knet: no visible global function definition for 'hist'
plot.Knet: no visible global function definition for 'abline'
Undefined global functions or variables:
abline hist lines par plot pnorm polygon quantile runif sd
Consider adding
importFrom("graphics", "abline", "hist", "lines", "par", "plot",
"polygon")
importFrom("stats", "pnorm", "quantile", "runif", "sd")
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 ... 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-3.8-bioc/R/library/SANTA/libs/i386/SANTA.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 ...
** 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 'runTests.R'
OK
** running tests for arch 'x64' ...
Running 'runTests.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: 1 WARNING, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/SANTA.Rcheck/00check.log'
for details.
SANTA.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/SANTA_2.20.0.tar.gz && rm -rf SANTA.buildbin-libdir && mkdir SANTA.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SANTA.buildbin-libdir SANTA_2.20.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL SANTA_2.20.0.zip && rm SANTA_2.20.0.tar.gz SANTA_2.20.0.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 3759k 100 3759k 0 0 42.5M 0 --:--:-- --:--:-- --:--:-- 44.2M
install for i386
* installing *source* package 'SANTA' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c computenetK_fewzeros.c -o computenetK_fewzeros.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c computenetK_manyzeros.c -o computenetK_manyzeros.o
computenetK_manyzeros.c: In function 'computenetK_manyzeros':
computenetK_manyzeros.c:29:24: warning: assignment from incompatible pointer type
p_which_vw_nonzero = R_alloc(n_nonzero_vertices, sizeof(int));
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c computenodeAUK.c -o computenodeAUK.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c computeweights.c -o computeweights.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o SANTA.dll tmp.def computenetK_fewzeros.o computenetK_manyzeros.o computenodeAUK.o computeweights.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/SANTA.buildbin-libdir/SANTA/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'SANTA'
finding HTML links ... done
BinGraph html
Compactness html
CreateGrid html
DistGraph html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpakxESn/R.INSTALL1438115c1397/SANTA/man/DistGraph.Rd:53: file link 'shortest.paths' in package 'igraph' does not exist and so has been treated as a topic
GraphDiffusion html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpakxESn/R.INSTALL1438115c1397/SANTA/man/GraphDiffusion.Rd:45: file link 'shortest.paths' in package 'igraph' does not exist and so has been treated as a topic
GraphMFPT html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpakxESn/R.INSTALL1438115c1397/SANTA/man/GraphMFPT.Rd:46: file link 'shortest.paths' in package 'igraph' does not exist and so has been treated as a topic
Knet html
Knode html
SANTA.data html
SpreadHits html
plot.Knet html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'SANTA' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c computenetK_fewzeros.c -o computenetK_fewzeros.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c computenetK_manyzeros.c -o computenetK_manyzeros.o
computenetK_manyzeros.c: In function 'computenetK_manyzeros':
computenetK_manyzeros.c:29:24: warning: assignment from incompatible pointer type
p_which_vw_nonzero = R_alloc(n_nonzero_vertices, sizeof(int));
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c computenodeAUK.c -o computenodeAUK.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c computeweights.c -o computeweights.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o SANTA.dll tmp.def computenetK_fewzeros.o computenetK_manyzeros.o computenodeAUK.o computeweights.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/SANTA.buildbin-libdir/SANTA/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SANTA' as SANTA_2.20.0.zip
* DONE (SANTA)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'SANTA' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
SANTA.Rcheck/tests_i386/runTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.
> BiocGenerics:::testPackage("SANTA")
Attaching package: 'igraph'
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
computing graph distance bins... done
computing graph distance bins... done
computing graph distance bins... done
computing graph distance bins... done
computing graph distance bins... done
computing graph distance bins... done
computing graph distance bins... done
computing graph distance bins... done
computing graph distance bins... done
computing graph distance bins... done
computing graph distance bins... done
computing graph distance bins... computing graph distance bins... computing graph distance bins... done
no edge attribute with name 'distance' found so all edge distances set to 1
computing graph distance matrix... done
no edge attribute with name 'distance' found so all edge distances set to 1
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
Warning: stack imbalance in '<-', 14 then 15
Warning: stack imbalance in '<-', 15 then 16
Warning: stack imbalance in '{', 10 then 12
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
RUNIT TEST PROTOCOL -- Sat Apr 13 05:20:01 2019
***********************************************
Number of test functions: 13
Number of errors: 0
Number of failures: 0
1 Test Suite :
SANTA RUnit Tests - 13 test functions, 0 errors, 0 failures
Number of test functions: 13
Number of errors: 0
Number of failures: 0
Warning messages:
1: In SANTA:::CheckAttributes(g, vertex.attr = "vertex.attr") :
non-numeric/non-logical vertex weights found and converted to numerals
2: In SpreadHits(g, h = 2, clusters = 3, distance.cutoff = 20, lambda = 10, :
seed vertices not identified
>
> proc.time()
user system elapsed
7.56 2.12 9.95
|
SANTA.Rcheck/tests_x64/runTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.
> BiocGenerics:::testPackage("SANTA")
Attaching package: 'igraph'
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
computing graph distance bins... done
computing graph distance bins... done
computing graph distance bins... done
computing graph distance bins... done
computing graph distance bins... done
computing graph distance bins... done
computing graph distance bins... done
computing graph distance bins... done
computing graph distance bins... done
computing graph distance bins... done
computing graph distance bins... done
computing graph distance bins... computing graph distance bins... computing graph distance bins... done
no edge attribute with name 'distance' found so all edge distances set to 1
computing graph distance matrix... done
no edge attribute with name 'distance' found so all edge distances set to 1
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
Warning: stack imbalance in '<-', 14 then 15
Warning: stack imbalance in '<-', 15 then 16
Warning: stack imbalance in '{', 10 then 12
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
computing graph distance matrix... done
RUNIT TEST PROTOCOL -- Sat Apr 13 05:20:12 2019
***********************************************
Number of test functions: 13
Number of errors: 0
Number of failures: 0
1 Test Suite :
SANTA RUnit Tests - 13 test functions, 0 errors, 0 failures
Number of test functions: 13
Number of errors: 0
Number of failures: 0
Warning messages:
1: In SANTA:::CheckAttributes(g, vertex.attr = "vertex.attr") :
non-numeric/non-logical vertex weights found and converted to numerals
2: In SpreadHits(g, h = 2, clusters = 3, distance.cutoff = 20, lambda = 10, :
seed vertices not identified
>
> proc.time()
user system elapsed
7.78 2.25 10.01
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SANTA.Rcheck/examples_i386/SANTA-Ex.timings
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SANTA.Rcheck/examples_x64/SANTA-Ex.timings
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