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This page was generated on 2023-10-20 09:38:00 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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Package 358/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cliqueMS 1.14.1  (landing page)
Oriol Senan Campos
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/cliqueMS
git_branch: RELEASE_3_17
git_last_commit: 7f3207e
git_last_commit_date: 2023-07-09 22:24:10 -0400 (Sun, 09 Jul 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for cliqueMS on kjohnson2


To the developers/maintainers of the cliqueMS package:
- 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.

raw results


Summary

Package: cliqueMS
Version: 1.14.1
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_1.14.1.tar.gz
StartedAt: 2023-10-17 10:02:38 -0400 (Tue, 17 Oct 2023)
EndedAt: 2023-10-17 10:11:18 -0400 (Tue, 17 Oct 2023)
EllapsedTime: 520.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: cliqueMS.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running 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_1.14.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/cliqueMS.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cliqueMS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cliqueMS’ version ‘1.14.1’
* 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 ... WARNING
Found the following significant warnings:
  ./annotationCliqueMSR.h:739:5: warning: variable 'completeroundscore' is uninitialized when used here [-Wuninitialized]
See ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/cliqueMS.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* 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 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  6.635  1.371  13.203
createanClique 5.393  1.181  10.534
anClique-class 5.657  0.624  10.390
computeCliques 4.033  0.718   7.636
getCliques     3.475  0.674   6.654
anClique       3.052  0.644   6.046
* 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 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/cliqueMS.Rcheck/00check.log’
for details.



Installation output

cliqueMS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL cliqueMS
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘cliqueMS’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
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/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include     -fPIC  -falign-functions=64 -Wall -g -O2  -c findCliquesR.cpp -o findCliquesR.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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 -single_module -multiply_defined suppress -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-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: could not create compact unwind for ___emutls_get_address: registers 23 and 24 not saved contiguously in frame
installing to /Library/Frameworks/R.framework/Versions/4.3-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)

Tests output

cliqueMS.Rcheck/tests/testthat.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 145 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 
 22.157   2.048  39.302 

Example timings

cliqueMS.Rcheck/cliqueMS-Ex.timings

nameusersystemelapsed
anClique-class 5.657 0.62410.390
anClique3.0520.6446.046
computeCliques4.0330.7187.636
createNetwork 6.635 1.37113.203
createanClique 5.393 1.18110.534
getAnnotation0.2060.0300.344
getCliques3.4750.6746.654
getIsotopes0.0770.0040.139