Oriol Senan Campos
| Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/cliqueMS |
| git_branch: RELEASE_3_21 |
| git_last_commit: c7c2873 |
| git_last_commit_date: 2025-04-15 13:38:55 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-16 11:40 -0400 (Thu, 16 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
| 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 373/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| cliqueMS 1.22.0 (landing page) Oriol Senan Campos
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / 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. |
| Package: cliqueMS |
| Version: 1.22.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cliqueMS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cliqueMS_1.22.0.tar.gz |
| StartedAt: 2025-10-14 16:21:45 -0400 (Tue, 14 Oct 2025) |
| EndedAt: 2025-10-14 16:28:57 -0400 (Tue, 14 Oct 2025) |
| EllapsedTime: 431.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: cliqueMS.Rcheck |
| Warnings: 1 |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cliqueMS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cliqueMS_1.22.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/cliqueMS.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cliqueMS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cliqueMS’ version ‘1.22.0’
* 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 ... WARNING
Found the following significant warnings:
./annotationCliqueMSR.h:739:5: warning: variable 'completeroundscore' is uninitialized when used here [-Wuninitialized]
See ‘/Users/biocbuild/bbs-3.21-bioc/meat/cliqueMS.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* 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 code 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 9.156 2.589 11.812
anClique-class 8.981 1.500 10.610
createanClique 7.787 2.303 10.170
computeCliques 5.738 0.543 6.333
anClique 4.173 1.608 5.838
getCliques 5.027 0.405 5.510
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.21-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/Resources/bin/R CMD INSTALL cliqueMS
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘cliqueMS’ ...
** this is package ‘cliqueMS’ version ‘1.22.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -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++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c findCliquesR.cpp -o findCliquesR.o
In file included from findCliquesR.cpp:2:
In file included from ./networkCliqueMSR.h:7:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include/RcppArmadilloExtensions/sample.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include/RcppArmadilloExtensions/fixprob.h:24:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:17: warning: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more. [-W#pragma-messages]
#pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
^
1 warning generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c findIsotopesR.cpp -o findIsotopesR.o
clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o cliqueMS.so RcppExports.o findAnnotationR.o findCliquesR.o findIsotopesR.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/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 version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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 145 rounds
Kernighan-Lin done with 2 rounds
Finishing value of logl is -164.568
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 14 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 14 ]
>
> proc.time()
user system elapsed
31.416 3.893 35.704
cliqueMS.Rcheck/cliqueMS-Ex.timings
| name | user | system | elapsed | |
| anClique-class | 8.981 | 1.500 | 10.610 | |
| anClique | 4.173 | 1.608 | 5.838 | |
| computeCliques | 5.738 | 0.543 | 6.333 | |
| createNetwork | 9.156 | 2.589 | 11.812 | |
| createanClique | 7.787 | 2.303 | 10.170 | |
| getAnnotation | 0.256 | 0.062 | 0.320 | |
| getCliques | 5.027 | 0.405 | 5.510 | |
| getIsotopes | 0.127 | 0.005 | 0.134 | |