Alex J. Cornish
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 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 2019-04-16 11:56:47 -0400 (Tue, 16 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 | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: SANTA |
| Version: 2.20.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SANTA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SANTA_2.20.0.tar.gz |
| StartedAt: 2019-04-16 02:36:31 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 02:37:39 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 67.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: SANTA.Rcheck |
| Warnings: 1 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SANTA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SANTA_2.20.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/SANTA.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* 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 ... 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 for sufficient/correct file permissions ... OK
* checking whether package ‘SANTA’ can be installed ... WARNING
Found the following significant warnings:
computenetK_manyzeros.c:29:24: warning: incompatible pointer types assigning to 'int *' from 'char *' [-Wincompatible-pointer-types]
See ‘/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
* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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
‘/Users/biocbuild/bbs-3.8-bioc/meat/SANTA.Rcheck/00check.log’
for details.
SANTA.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SANTA
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘SANTA’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c computenetK_fewzeros.c -o computenetK_fewzeros.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c computenetK_manyzeros.c -o computenetK_manyzeros.o
computenetK_manyzeros.c:29:24: warning: incompatible pointer types assigning to 'int *' from 'char *' [-Wincompatible-pointer-types]
p_which_vw_nonzero = R_alloc(n_nonzero_vertices, sizeof(int));
^ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c computenodeAUK.c -o computenodeAUK.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c computeweights.c -o computeweights.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o SANTA.so computenetK_fewzeros.o computenetK_manyzeros.o computenodeAUK.o computeweights.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/SANTA/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SANTA)
SANTA.Rcheck/tests/runTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 -- Tue Apr 16 02:37:33 2019
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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
10.713 3.221 14.013
SANTA.Rcheck/SANTA-Ex.timings
| name | user | system | elapsed | |
| BinGraph | 0.253 | 0.029 | 0.283 | |
| CreateGrid | 0.036 | 0.003 | 0.039 | |
| DistGraph | 0.030 | 0.002 | 0.033 | |
| GraphDiffusion | 0.015 | 0.001 | 0.015 | |
| GraphMFPT | 0.047 | 0.001 | 0.049 | |
| Knet | 0.066 | 0.005 | 0.071 | |
| Knode | 0.019 | 0.001 | 0.021 | |
| SANTA.data | 0.028 | 0.005 | 0.034 | |
| SpreadHits | 0.030 | 0.002 | 0.032 | |
| plot.Knet | 0.048 | 0.005 | 0.053 | |