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This page was generated on 2022-01-24 13:05:22 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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

INSTALL results for MSnbase on nebbiolo2


To the developers/maintainers of the MSnbase package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MSnbase.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1222/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSnbase 2.20.4  (landing page)
Laurent Gatto
Snapshot Date: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/MSnbase
git_branch: RELEASE_3_14
git_last_commit: c86ac8b
git_last_commit_date: 2022-01-13 12:09:21 -0500 (Thu, 13 Jan 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: MSnbase
Version: 2.20.4
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL MSnbase
StartedAt: 2022-01-23 03:22:15 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 03:23:00 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 45.5 seconds
RetCode: 0
Status:   OK  

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL MSnbase
###
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘MSnbase’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c Spectrum1_class.c -o Spectrum1_class.o
Spectrum1_class.c:8:13: warning: ‘_new_Spectrum1’ defined but not used [-Wunused-function]
    8 | static SEXP _new_Spectrum1(SEXP msLevel, SEXP peaksCount, SEXP rt,
      |             ^~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c Spectrum2_class.c -o Spectrum2_class.o
Spectrum2_class.c:9:13: warning: ‘_new_Spectrum2’ defined but not used [-Wunused-function]
    9 | static SEXP _new_Spectrum2(SEXP msLevel, SEXP peaksCount, SEXP rt,
      |             ^~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c imp_neighbour_avg.cpp -o imp_neighbour_avg.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c utils.c -o utils.o
utils.c: In function ‘compar_double_dd_for_stable_asc_order’:
utils.c:92:15: warning: unused variable ‘ret’ [-Wunused-variable]
   92 |   int i1, i2, ret;
      |               ^~~
utils.c: In function ‘compar_double_dd_for_stable_desc_order’:
utils.c:107:15: warning: unused variable ‘ret’ [-Wunused-variable]
  107 |   int i1, i2, ret;
      |               ^~~
utils.c: In function ‘compar_double_asc_order’:
utils.c:123:18: warning: unused variable ‘ret’ [-Wunused-variable]
  123 |   double d1, d2, ret;
      |                  ^~~
utils.c: In function ‘compar_double_desc_order’:
utils.c:133:18: warning: unused variable ‘ret’ [-Wunused-variable]
  133 |   double d1, d2, ret;
      |                  ^~~
At top level:
utils.c:131:12: warning: ‘compar_double_desc_order’ defined but not used [-Wunused-function]
  131 | static int compar_double_desc_order(const void *p1, const void *p2)
      |            ^~~~~~~~~~~~~~~~~~~~~~~~
utils.c:121:12: warning: ‘compar_double_asc_order’ defined but not used [-Wunused-function]
  121 | static int compar_double_asc_order(const void *p1, const void *p2)
      |            ^~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o MSnbase.so RcppExports.o Spectrum1_class.o Spectrum2_class.o imp_neighbour_avg.o utils.o -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-MSnbase/00new/MSnbase/libs
** R
** data
*** moving datasets to lazyload DB
Creating a new generic function for ‘trimws’ in package ‘MSnbase’
in method for ‘coerce’ with signature ‘"MSnSet","SummarizedExperiment"’: no definition for class “SummarizedExperiment”
in method for ‘coerce’ with signature ‘"SummarizedExperiment","MSnSet"’: no definition for class “SummarizedExperiment”
in method for ‘coerce’ with signature ‘"IBSpectra","MSnSet"’: no definition for class “IBSpectra”
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘trimws’ in package ‘MSnbase’
in method for ‘coerce’ with signature ‘"MSnSet","SummarizedExperiment"’: no definition for class “SummarizedExperiment”
in method for ‘coerce’ with signature ‘"SummarizedExperiment","MSnSet"’: no definition for class “SummarizedExperiment”
in method for ‘coerce’ with signature ‘"IBSpectra","MSnSet"’: no definition for class “IBSpectra”
** 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 (MSnbase)