| Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-03-16 10:55:28 -0400 (Thu, 16 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" | 4540 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4290 |
| 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 cliqueMS package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cliqueMS.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 353/2189 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| cliqueMS 1.13.0 (landing page) Oriol Senan Campos
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
| Package: cliqueMS |
| Version: 1.13.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:cliqueMS.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings cliqueMS_1.13.0.tar.gz |
| StartedAt: 2023-03-15 19:24:00 -0400 (Wed, 15 Mar 2023) |
| EndedAt: 2023-03-15 19:28:55 -0400 (Wed, 15 Mar 2023) |
| EllapsedTime: 294.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: cliqueMS.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:cliqueMS.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings cliqueMS_1.13.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/cliqueMS.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘cliqueMS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cliqueMS’ version ‘1.13.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘cliqueMS’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* 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 ... NOTE
Namespace in Imports field not imported from: ‘MSnbase’
All declared Imports should be used.
* 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 6.923 1.705 8.416
anClique-class 6.064 0.731 6.735
computeCliques 4.465 1.020 5.698
getCliques 4.025 1.239 5.157
createanClique 3.294 1.223 7.438
* 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 ...
‘annotate_features.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/cliqueMS.Rcheck/00check.log’
for details.
cliqueMS.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL cliqueMS
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘cliqueMS’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c findAnnotationR.cpp -o findAnnotationR.o
In file included from findAnnotationR.cpp:1:
annotationCliqueMSR.h: In function ‘std::vector<std::pair<double, double> > sortMass(annotData&, int, std::unordered_map<double, std::pair<double, double> >, int)’:
annotationCliqueMSR.h:440:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::pair<double, double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
440 | if(id < allM.size()) // not add more masses in case that for that feature are less than "n" top masses
| ~~~^~~~~~~~~~~~~
annotationCliqueMSR.h: In function ‘std::unordered_set<double> getTopScoringMasses(annotData&, int, rawadList, int, int, double)’:
annotationCliqueMSR.h:476:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::pair<double, double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
476 | if(id < allM.size()) // not add more masses in case that there are less than "n" top masses
| ~~~^~~~~~~~~~~~~
annotationCliqueMSR.h: In function ‘std::vector<int> sortAnnotations(std::unordered_map<int, Annotation>&, int)’:
annotationCliqueMSR.h:725:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::pair<double, int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
725 | if(id < allAn.size() )
| ~~~^~~~~~~~~~~~~~
annotationCliqueMSR.h: In function ‘double computeMaxScore(std::vector<double>&, int, double)’:
annotationCliqueMSR.h:747:25: warning: ‘completeroundscore’ may be used uninitialized in this function [-Wmaybe-uninitialized]
747 | score = (completeround*completeroundscore) + remainderroundscore + (completeround*newmass);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c findCliquesR.cpp -o findCliquesR.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c findIsotopesR.cpp -o findIsotopesR.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o cliqueMS.so RcppExports.o findAnnotationR.o findCliquesR.o findIsotopesR.o -fopenmp -llapack -L/home/biocbuild/bbs-3.17-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/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) (2023-01-10 r83596) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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
Beggining value of logl is -712.347
Aggregate cliques done, with 144 rounds
Kernighan-Lin done with 2 rounds
Finishing value of logl is -164.568
[ FAIL 0 | WARN 38 | SKIP 0 | PASS 14 ]
[ FAIL 0 | WARN 38 | SKIP 0 | PASS 14 ]
>
> proc.time()
user system elapsed
21.522 2.337 23.877
cliqueMS.Rcheck/cliqueMS-Ex.timings
| name | user | system | elapsed | |
| anClique-class | 6.064 | 0.731 | 6.735 | |
| anClique | 3.459 | 0.974 | 4.391 | |
| computeCliques | 4.465 | 1.020 | 5.698 | |
| createNetwork | 6.923 | 1.705 | 8.416 | |
| createanClique | 3.294 | 1.223 | 7.438 | |
| getAnnotation | 2.485 | 0.799 | 0.213 | |
| getCliques | 4.025 | 1.239 | 5.157 | |
| getIsotopes | 0.075 | 0.000 | 0.075 | |