Oriol Senan Campos
| Snapshot Date: 2024-01-16 14:00:13 -0500 (Tue, 16 Jan 2024) |
| git_url: https://git.bioconductor.org/packages/cliqueMS |
| git_branch: devel |
| git_last_commit: b59b661 |
| git_last_commit_date: 2023-10-24 11:18:13 -0500 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-01-17 12:23:58 -0500 (Wed, 17 Jan 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4330 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4289 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2023-11-11 r85510) -- "Unsuffered Consequences" | 4413 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2023-11-01 r85459) -- "Unsuffered Consequences" | 4341 |
| 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 | ||||
| Package 361/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| cliqueMS 1.17.0 (landing page) Oriol Senan Campos
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | ERROR | ERROR | skipped | skipped | |||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the cliqueMS package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: cliqueMS |
| Version: 1.17.0 |
| Command: /home/biocbuild/R/R-4.4-devel-2023.11.02/bin/R CMD check --install=check:cliqueMS.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library --no-vignettes --timings cliqueMS_1.17.0.tar.gz |
| StartedAt: 2024-01-17 04:07:32 -0000 (Wed, 17 Jan 2024) |
| EndedAt: 2024-01-17 04:15:21 -0000 (Wed, 17 Jan 2024) |
| EllapsedTime: 468.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: cliqueMS.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/R/R-4.4-devel-2023.11.02/bin/R CMD check --install=check:cliqueMS.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library --no-vignettes --timings cliqueMS_1.17.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/cliqueMS.Rcheck’
* using R Under development (unstable) (2023-11-01 r85459)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cliqueMS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cliqueMS’ version ‘1.17.0’
* 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++ (GCC) 10.3.1’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
installed size is 9.7Mb
sub-directories of 1Mb or more:
libs 8.0Mb
* 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 loading without being on the library search path ... 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 9.423 3.923 13.151
anClique-class 8.573 1.149 9.639
getCliques 5.248 2.618 7.746
computeCliques 5.615 1.544 7.057
createanClique 4.190 1.859 11.266
getAnnotation 3.746 2.025 0.288
anClique 4.362 1.373 5.621
* 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: 4 NOTEs
See
‘/home/biocbuild/bbs-3.19-bioc/meat/cliqueMS.Rcheck/00check.log’
for details.
cliqueMS.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/R/R-4.4-devel-2023.11.02/bin/R CMD INSTALL cliqueMS
###
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* installing to library ‘/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library’
* installing *source* package ‘cliqueMS’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/R/R-devel/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/BH/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-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/R/R-devel/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/BH/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-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:739:24: warning: ‘completeroundscore’ may be used uninitialized in this function [-Wmaybe-uninitialized]
739 | completeroundscore += *ritv;
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/R/R-devel/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/BH/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-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/R/R-devel/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/BH/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-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/R/R-devel/lib -L/usr/local/lib -o cliqueMS.so RcppExports.o findAnnotationR.o findCliquesR.o findIsotopesR.o -fopenmp -lopenblas -lgfortran -lm -L/home/biocbuild/R/R-devel/lib -lR
installing to /home/biocbuild/R/R-4.4-devel-2023.11.02/site-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) (2023-11-01 r85459) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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 0 | SKIP 0 | PASS 14 ]
>
> proc.time()
user system elapsed
31.674 3.479 34.939
cliqueMS.Rcheck/cliqueMS-Ex.timings
| name | user | system | elapsed | |
| anClique-class | 8.573 | 1.149 | 9.639 | |
| anClique | 4.362 | 1.373 | 5.621 | |
| computeCliques | 5.615 | 1.544 | 7.057 | |
| createNetwork | 9.423 | 3.923 | 13.151 | |
| createanClique | 4.190 | 1.859 | 11.266 | |
| getAnnotation | 3.746 | 2.025 | 0.288 | |
| getCliques | 5.248 | 2.618 | 7.746 | |
| getIsotopes | 0.093 | 0.000 | 0.093 | |