Oriol Senan Campos
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/cliqueMS |
| Branch: master |
| Last Commit: 9368dc6 |
| Last Changed Date: 2019-11-12 12:48:21 -0500 (Tue, 12 Nov 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:56:06 -0500 (Thu, 16 Jan 2020).
| Package 300/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| cliqueMS 1.1.1 Oriol Senan Campos
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: cliqueMS |
| Version: 1.1.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cliqueMS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cliqueMS_1.1.1.tar.gz |
| StartedAt: 2020-01-16 02:56:44 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 03:05:13 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 508.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: cliqueMS.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cliqueMS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cliqueMS_1.1.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/cliqueMS.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cliqueMS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cliqueMS’ version ‘1.1.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘cliqueMS’ 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
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
createNetwork 10.755 0.307 11.110
createanClique 9.158 0.281 9.505
anClique-class 7.549 0.462 8.713
computeCliques 6.933 0.359 7.373
getCliques 5.634 0.153 5.799
anClique 5.374 0.145 6.101
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.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 NOTE
See
‘/Users/biocbuild/bbs-3.11-bioc/meat/cliqueMS.Rcheck/00check.log’
for details.
cliqueMS.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL cliqueMS
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘cliqueMS’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c findAnnotationR.cpp -o findAnnotationR.o
In file included from findAnnotationR.cpp:1:
./annotationCliqueMSR.h:739:5: warning: variable 'completeroundscore' is uninitialized when used here [-Wuninitialized]
completeroundscore += *ritv;
^~~~~~~~~~~~~~~~~~
./annotationCliqueMSR.h:733:28: note: initialize the variable 'completeroundscore' to silence this warning
double completeroundscore,remainderroundscore = 0;
^
= 0.0
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c findCliquesR.cpp -o findCliquesR.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c findIsotopesR.cpp -o findIsotopesR.o
clang++ -std=gnu++11 -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 cliqueMS.so RcppExports.o findAnnotationR.o findCliquesR.o findIsotopesR.o -fopenmp -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-cliqueMS/00new/cliqueMS/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (cliqueMS)
cliqueMS.Rcheck/tests/testthat.Rout
R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
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.
> library(testthat)
> library(cliqueMS)
>
> test_check("cliqueMS")
adduct log10freq massdiff nummol charge
1 [M+2H-NH3]2+ -3.5129044 -15.012016600 1 2
2 [Cat]3+ -3.5129044 -0.001645737 1 3
3 [Cat]2+ -3.5129044 -0.001040400 1 2
4 [Cat+H]2+ -3.3368132 1.006178842 1 2
5 [M+2H]2+ -1.8139344 2.014552000 1 2
6 [M+H+Na]2+ -2.6999911 23.996494000 1 2
7 [M+2H+Na]3+ -3.8139344 25.003770000 1 3
8 [M+H+K]2+ -2.2341508 39.970434000 1 2
9 [M+2Na]2+ -2.6678064 45.978436000 1 2
10 [M+H+2Na]3+ -3.5129044 46.985730000 1 3
11 [M+3Na]3+ -3.5129044 68.967654000 1 3
12 [M+H]+ -0.2689987 1.007276000 1 1
13 [M+H-H2O]+ -0.7476085 -17.003277800 1 1
14 [M+Na]+ -0.9632882 22.989218000 1 1
15 [M+H-NH3]+ -1.5886251 -16.019274320 1 1
16 [M-H+2Na]+ -1.8596919 44.971164440 1 1
17 [Cat]+ -1.8948563 -0.000548579 1 1
18 [M-2H+3Na]+ -1.9108444 66.953081400 1 1
19 [M+H+H2O]+ -2.3225727 19.017868210 1 1
20 [M+K]+ -2.4159944 38.963158000 1 1
21 [M+NH4]+ -2.4917151 18.033823000 1 1
22 [M-H+2K]+ -3.1149644 76.919040000 1 1
23 [Cat+H2O]+ -3.2118744 18.010011000 1 1
24 [M+H-OH]+ -3.2118744 -15.995481930 1 1
25 [Cat-H2O]+ -3.5129044 -18.011087900 1 1
26 [Cat-H]+ -3.5129044 -1.008340400 1 1
27 [M+Na-H2O]+ -3.5129044 4.978142219 1 1
28 [M-2H+3K]+ -3.5129044 114.874881400 1 1
29 [M+K-H2O]+ -3.8139344 20.952042220 1 1
30 [M-CO2H+H]+ -4.8139344 -43.989863780 1 1
31 [3M+H-H2O]+ -4.8139344 -17.003277800 3 1
32 [2M+H]+ -1.2239848 1.007276000 2 1
33 [3M+H]+ -2.2698664 1.007276000 3 1
34 [2M+Na-H2O]+ -3.8139344 4.978142219 2 1
35 [2M+K-H2O]+ -3.8139344 20.952042220 2 1
36 [3M+K-H2O]+ -4.8139344 20.952042220 3 1
37 [2M+Na]+ -2.9688364 22.989218000 2 1
38 [2M+K]+ -3.8139344 38.963142220 2 1
39 [3M+K]+ -3.8139344 38.963142220 3 1
[1] -1.31290442 -1.31290442 -1.31290442 -1.13681316 0.38606558 -0.49999107
[7] -1.61393442 -0.03415082 -0.46780638 -1.31290442 -1.31290442 1.93100135
[13] 1.45239151 1.23671182 0.61137486 0.34030809 0.30514367 0.28915557
[19] -0.12257272 -0.21599441 -0.29171512 -0.91496441 -1.01187443 -1.01187443
[25] -1.31290442 -1.31290442 -1.31290442 -1.31290442 -1.61393442 -2.61393442
[31] -2.61393442 0.97601518 -0.06986637 -1.61393442 -1.61393442 -2.61393442
[37] -0.76883638 -1.61393442 -1.61393442
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Beggining value of logl is -722.284
Aggregate cliques done, with 145 rounds
Kernighan-Lin done with 2 rounds
Finishing value of logl is -161.574
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══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 14 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
36.216 2.506 40.444
cliqueMS.Rcheck/cliqueMS-Ex.timings
| name | user | system | elapsed | |
| anClique-class | 7.549 | 0.462 | 8.713 | |
| anClique | 5.374 | 0.145 | 6.101 | |
| computeCliques | 6.933 | 0.359 | 7.373 | |
| createNetwork | 10.755 | 0.307 | 11.110 | |
| createanClique | 9.158 | 0.281 | 9.505 | |
| getAnnotation | 0.608 | 0.007 | 1.043 | |
| getCliques | 5.634 | 0.153 | 5.799 | |
| getIsotopes | 0.282 | 0.004 | 0.286 | |