[Bioc-devel] Error when building BgeeCall package on Mac OS

[Martin Morgan]

I added a response to your issue at

  https://github.com/Bioconductor/Contributions/issues/1002#issuecomment-478991986

encouraging you (again) to avoid installing software on the user system; there are basic problems with this approach, and the correct solution is to list kallisto as a SystemDependency: in your DESCRIPTION file.

Maritn

On 4/2/19, 4:17 AM, "Bioc-devel on behalf of Julien Wollbrett" <bioc-devel-bounces using r-project.org on behalf of julien.wollbrett using sib.swiss> wrote:

    Hello,
    
    My package (called BgeeCall) is under review and passed R CMD Build and 
    R CMD Check for Linux and windows.
    
    I still have an error on Mac. I tried to reproduce it using different 
    versions of R (3.5 and 3.6) and different OS
    
    versions (Sierra and El Capitan). I tried on 5 different computers but 
    still not able to reproduce this error.
    
    Does anyone have any idea on the origin of this error ? What should I 
    try to do to solve it?
    
    dyld: Library not loaded: @rpath/libz.1.dylib
       Referenced from: /private/var/folders/gh/37kcv9bj20v2qnpgxq14hh1c0000gq/T/Rtmp7eA44u/Rbuild1406e51fd6e7f/BgeeCall/kallisto/kallisto
       Reason: image not found
    Will run kallisto using this command line : /private/var/folders/gh/37kcv9bj20v2qnpgxq14hh1c0000gq/T/Rtmp7eA44u/Rbuild1406e51fd6e7f/BgeeCall/kallisto/kallisto quant -i /private/var/folders/gh/37kcv9bj20v2qnpgxq14hh1c0000gq/T/Rtmp7eA44u/Rbuild1406e51fd6e7f/BgeeCall/intergenic_0.1/6239/kallisto/transcriptome_WBcel235/transcriptome.idx -o /private/var/folders/gh/37kcv9bj20v2qnpgxq14hh1c0000gq/T/Rtmp7eA44u/Rbuild1406e51fd6e7f/BgeeCall/intergenic_0.1/6239/kallisto/transcriptome_WBcel235/annotation_WBcel235_84/SRX099901_subset -t 1 --single -l 180 -s 30 --bias  /private/var/folders/gh/37kcv9bj20v2qnpgxq14hh1c0000gq/T/Rtmp7eA44u/Rinst1406e55617de6/BgeeCall/extdata/SRX099901_subset/SRR350955_subset.fastq.gz
    dyld: Library not loaded: @rpath/libz.1.dylib
       Referenced from: /private/var/folders/gh/37kcv9bj20v2qnpgxq14hh1c0000gq/T/Rtmp7eA44u/Rbuild1406e51fd6e7f/BgeeCall/kallisto/kallisto
       Reason: image not found
    
    You can access to the submission issue here :
    
    https://github.com/Bioconductor/Contributions/issues/1002
    
    Thank you for your answers.
    
    
    Julien Wollbrett
    
    
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