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dozmorovlab / HiCcompare

Joint normalization of two Hi-C matrices, visualization and detection of differential chromatin interactions. See multiHiCcompare for the analysis of multiple Hi-C matrices
https://dozmorovlab.github.io/HiCcompare/
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Issue installing HiCcompare #26

Closed hannahdevens closed 1 year ago

hannahdevens commented 1 year ago

Hi, I am interested in using HiCcompare for a project I am working on, but I am having difficulty installing it in R using either of the 2 methods suggested on GitHub. When I try installing via BiocManager, I get the following error: Error: package or namespace load failed for ‘HiCcompare’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/Library/Frameworks/R.framework/Versions/4.2/Resources/library/DNAcopy/libs/DNAcopy.so': dlopen(/Library/Frameworks/R.framework/Versions/4.2/Resources/library/DNAcopy/libs/DNAcopy.so, 0x0006): Symbol not found: (__gfortran_os_error_at) Referenced from: '/Library/Frameworks/R.framework/Versions/4.2/Resources/library/DNAcopy/libs/DNAcopy.so' Expected in: '/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgfortran.5.dylib’

When I try installing via GitHub, I get this error: ERROR: package installation failed Error: Failed to install 'HiCcompare' from GitHub: ! System command 'R’ failed

Do you have any ideas about what is going wrong? I am using R 4.2.

mdozmorov commented 1 year ago

Update 2022-11-28:

devtools::install_github("dozmorovlab/HiCcompare")

will install the package. The function get_CNV() has been disabled, as well as the QDNAseq package that depends on DNAcopy and gfortran. This function won't affect functionality, it is an auxiliary function to detect CNVs from BAM files.

Updating Bioconductor will take more work. But as of now, HiCcompare is installable.

hannahdevens commented 1 year ago

Thanks so much!