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This page was generated on 2022-01-17 11:07:08 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4161
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4056
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3998
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4115
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

BUILD BIN results for deepSNV on riesling1


To the developers/maintainers of the deepSNV package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/deepSNV.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 473/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
deepSNV 1.41.0  (landing page)
Moritz Gerstung
Snapshot Date: 2022-01-16 13:55:18 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/deepSNV
git_branch: master
git_last_commit: e79bce8
git_last_commit_date: 2021-10-26 12:01:57 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'IRanges' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: deepSNV
Version: 1.41.0
Command: rm -rf deepSNV.buildbin-libdir && mkdir deepSNV.buildbin-libdir && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --build --library=deepSNV.buildbin-libdir deepSNV_1.41.0.tar.gz
StartedAt: 2022-01-16 20:54:35 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 20:55:44 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 68.8 seconds
RetCode: 0
Status:   OK  
PackageFile: deepSNV_1.41.0.zip
PackageFileSize: 3.986 MiB

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf deepSNV.buildbin-libdir && mkdir deepSNV.buildbin-libdir && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --build --library=deepSNV.buildbin-libdir deepSNV_1.41.0.tar.gz
###
##############################################################################
##############################################################################


* installing *source* package 'deepSNV' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c bam2R.cpp -o bam2R.o
bam2R.cpp: In function 'int bam2R(char**, char**, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*)':
bam2R.cpp:97:13: warning: unused variable 'iter' [-Wunused-variable]
  hts_itr_t *iter = NULL;
             ^~~~
bam2R.cpp:100:6: warning: unused variable 'c' [-Wunused-variable]
  int c = 0;
      ^
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c betabinom.c -o betabinom.o
betabinom.c: In function 'pbb':
betabinom.c:27:9: warning: unused variable 'log' [-Wunused-variable]
  int i, log=0;
         ^~~
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o deepSNV.dll tmp.def bam2R.o betabinom.o D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -LC:/extsoft/lib/x64 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/meat/deepSNV.buildbin-libdir/00LOCK-deepSNV/00new/deepSNV/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'deepSNV'
    finding HTML links ... done
    Extract-methods                         html  
    RCC                                     html  
    RF                                      html  
    bam2R                                   html  
    betabinLRT                              html  
    bf2Vcf                                  html  
    finding level-2 HTML links ... done

    consensusSequence-methods               html  
    control-methods                         html  
    coordinates-methods                     html  
    counts                                  html  
    dbetabinom                              html  
    deepSNV-class                           html  
    deepSNV-methods                         html  
    deepSNV-package                         html  
    estimateDirichlet-methods               html  
    estimateDispersion-methods              html  
    estimateRho                             html  
    loadAllData                             html  
    makePrior                               html  
    manhattanPlot                           html  
    mcChunk                                 html  
    normalize-methods                       html  
    p.combine                               html  
    p.val-methods                           html  
    pbetabinom                              html  
    phiX                                    html  
    pi                                      html  
    plot.deepSNV                            html  
    qvals2Vcf                               html  
    repeatMask-methods                      html  
    shearwater                              html  
    show-deepSNV-method                     html  
    summary-methods                         html  
    test-methods                            html  
    trueSNVs                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'deepSNV' as deepSNV_1.41.0.zip
* DONE (deepSNV)