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RajLabMSSM / echolocatoR

Automated statistical and functional fine-mapping pipeline with extensive API access to datasets.
https://rajlabmssm.github.io/echolocatoR
MIT License
30 stars 11 forks source link

Installation Errors #122

Closed vermaa1 closed 1 year ago

vermaa1 commented 1 year ago

Hi,

I am getting many errors while installing the latest version of the package.

Here are the last few lines from the terminal output:


Creating a new generic function for ‘packageName’ in package ‘AnnotationDbi’
Creating a generic function for ‘ls’ from package ‘base’ in package ‘AnnotationDbi’                                                                           
Creating a generic function for ‘eapply’ from package ‘base’ in package ‘AnnotationDbi’                                                                       
Creating a generic function for ‘exists’ from package ‘base’ in package ‘AnnotationDbi’                                                                       
Creating a generic function for ‘sample’ from package ‘base’ in package ‘AnnotationDbi’                                                                       
** help
*** installing help indices
** 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
* DONE (AnnotationDbi)
ERROR: dependency ‘XML’ is not available for package ‘biomaRt’
* removing ‘/autofs/nccs-svm1_home1/anuragv/.conda/envs/echoverse/lib/R/library/biomaRt’                                                                      
ERROR: dependencies ‘XML’, ‘restfulr’ are not available for package ‘rtracklayer’                                                                             
* removing ‘/autofs/nccs-svm1_home1/anuragv/.conda/envs/echoverse/lib/R/library/rtracklayer’                                                                  
ERROR: dependencies ‘rtracklayer’, ‘biomaRt’ are not available for package ‘GenomicFeatures’                                                                  
* removing ‘/autofs/nccs-svm1_home1/anuragv/.conda/envs/echoverse/lib/R/library/GenomicFeatures’                                                              
ERROR: dependency ‘rtracklayer’ is not available for package ‘BSgenome’
* removing ‘/autofs/nccs-svm1_home1/anuragv/.conda/envs/echoverse/lib/R/library/BSgenome’                                                                     
ERROR: dependencies ‘rtracklayer’, ‘BSgenome’, ‘GenomicFeatures’ are not available for package ‘VariantAnnotation’                                            
* removing ‘/autofs/nccs-svm1_home1/anuragv/.conda/envs/echoverse/lib/R/library/VariantAnnotation’                                                            
ERROR: dependencies ‘BSgenome’, ‘VariantAnnotation’, ‘rtracklayer’ are not available for package ‘MungeSumstats’                                              
* removing ‘/autofs/nccs-svm1_home1/anuragv/.conda/envs/echoverse/lib/R/library/MungeSumstats’                                                                

The downloaded source packages are in
        ‘/tmp/RtmpQE2e9e/downloaded_packages’
Downloading GitHub repo RajLabMSSM/echoconda@HEAD
Skipping echoconda, it is already being installed
Downloading GitHub repo RajLabMSSM/downloadR@HEAD
Skipping downloadR, it is already being installed
Downloading GitHub repo RajLabMSSM/echodata@HEAD
Skipping echodata, it is already being installed
Downloading GitHub repo RajLabMSSM/echotabix@HEAD
Skipping echotabix, it is already being installed
Downloading GitHub repo RajLabMSSM/echoannot@HEAD
Skipping echoannot, it is already being installed
Downloading GitHub repo RajLabMSSM/catalogueR@HEAD
Skipping catalogueR, it is already being installed
Downloading GitHub repo RajLabMSSM/echoLD@HEAD
Skipping echoLD, it is already being installed
Downloading GitHub repo RajLabMSSM/echofinemap@HEAD
Skipping echofinemap, it is already being installed
Downloading GitHub repo RajLabMSSM/echoplot@HEAD
Skipping echoplot, it is already being installed
Skipping install of 'echodeps' from a github remote, the SHA1 (2a0ccae6) has not changed since last install.                                                  
  Use `force = TRUE` to force installation
Running `R CMD build`...
* checking for file ‘/tmp/RtmpQE2e9e/remotes36a274e7d28fd/RajLabMSSM-echolocatoR-b8dd387/DESCRIPTION’ ... OK                                                  
* preparing ‘echolocatoR’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Omitted ‘LazyData’ from DESCRIPTION
* building ‘echolocatoR_2.0.1.tar.gz’
ERROR: dependencies ‘echoconda’, ‘downloadR’, ‘echodata’, ‘echotabix’, ‘echoannot’, ‘catalogueR’, ‘echoLD’, ‘echofinemap’, ‘echoplot’ are not available for package ‘echolocatoR’
* removing ‘/autofs/nccs-svm1_home1/anuragv/.conda/envs/echoverse/lib/R/library/echolocatoR’

Based on the warning messages, it seems these packages failed to install:

Warning messages:
1: In i.p(...) : installation of package ‘XML’ had non-zero exit status
2: In i.p(...) : installation of package ‘restfulr’ had non-zero exit status
3: In i.p(...) : installation of package ‘biomaRt’ had non-zero exit status
4: In i.p(...) : installation of package ‘rtracklayer’ had non-zero exit status
5: In i.p(...) :
  installation of package ‘GenomicFeatures’ had non-zero exit status
6: In i.p(...) : installation of package ‘BSgenome’ had non-zero exit status
7: In i.p(...) :
  installation of package ‘VariantAnnotation’ had non-zero exit status
8: In i.p(...) : installation of package ‘MungeSumstats’ had non-zero exit status
9: In i.p(...) :
  installation of package ‘/tmp/RtmpQE2e9e/file36a27563b38e4/echodata_0.99.14.tar.gz’ had non-zero exit status
10: In i.p(...) :
  installation of package ‘/tmp/RtmpQE2e9e/file36a275ca1bb7f/echoconda_0.99.7.tar.gz’ had non-zero exit status
11: In i.p(...) :
  installation of package ‘/tmp/RtmpQE2e9e/file36a276594f92/downloadR_0.99.4.tar.gz’ had non-zero exit status
12: In i.p(...) : installation of package ‘XML’ had non-zero exit status
13: In i.p(...) : installation of package ‘restfulr’ had non-zero exit status
14: In i.p(...) : installation of package ‘biomaRt’ had non-zero exit status
15: In i.p(...) : installation of package ‘rtracklayer’ had non-zero exit status
16: In i.p(...) :
  installation of package ‘GenomicFeatures’ had non-zero exit status
17: In i.p(...) : installation of package ‘BSgenome’ had non-zero exit status
18: In i.p(...) :
  installation of package ‘VariantAnnotation’ had non-zero exit status
19: In i.p(...) :
  installation of package ‘MungeSumstats’ had non-zero exit status
20: In i.p(...) :
  installation of package ‘/tmp/RtmpQE2e9e/file36a272f10389b/echotabix_0.99.8.tar.gz’ had non-zero exit status
21: In i.p(...) : installation of package ‘XML’ had non-zero exit status
22: In i.p(...) : installation of package ‘restfulr’ had non-zero exit status
23: In i.p(...) : installation of package ‘biomaRt’ had non-zero exit status
24: In i.p(...) : installation of package ‘rtracklayer’ had non-zero exit status
25: In i.p(...) :
  installation of package ‘GenomicFeatures’ had non-zero exit status
26: In i.p(...) : installation of package ‘BSgenome’ had non-zero exit status
27: In i.p(...) : installation of package ‘ensembldb’ had non-zero exit status
28: In i.p(...) :
  installation of package ‘VariantAnnotation’ had non-zero exit status
29: In i.p(...) : installation of package ‘OrganismDbi’ had non-zero exit status
30: In i.p(...) : installation of package ‘biovizBase’ had non-zero exit status
31: In i.p(...) : installation of package ‘ggbio’ had non-zero exit status
32: In i.p(...) :
  installation of package ‘/tmp/RtmpQE2e9e/file36a2751ed251c/echoannot_0.99.7.tar.gz’ had non-zero exit status
33: In i.p(...) : installation of package ‘XML’ had non-zero exit status
34: In i.p(...) : installation of package ‘restfulr’ had non-zero exit status
35: In i.p(...) : installation of package ‘biomaRt’ had non-zero exit status
36: In i.p(...) : installation of package ‘rtracklayer’ had non-zero exit status
37: In i.p(...) :
  installation of package ‘GenomicFeatures’ had non-zero exit status
38: In i.p(...) : installation of package ‘ensembldb’ had non-zero exit status
39: In i.p(...) :
  installation of package ‘EnsDb.Hsapiens.v75’ had non-zero exit status
40: In i.p(...) :
  installation of package ‘/tmp/RtmpQE2e9e/file36a274c1cba21/catalogueR_1.0.0.tar.gz’ had non-zero exit status
41: In i.p(...) : installation of package ‘XML’ had non-zero exit status
42: In i.p(...) : installation of package ‘restfulr’ had non-zero exit status
43: In i.p(...) : installation of package ‘biomaRt’ had non-zero exit status
44: In i.p(...) : installation of package ‘rtracklayer’ had non-zero exit status
45: In i.p(...) :
  installation of package ‘GenomicFeatures’ had non-zero exit status
46: In i.p(...) : installation of package ‘BSgenome’ had non-zero exit status
47: In i.p(...) :
  installation of package ‘VariantAnnotation’ had non-zero exit status
48: In i.p(...) :
  installation of package ‘/tmp/RtmpQE2e9e/file36a272f247bf/echoLD_0.99.7.tar.gz’ had non-zero exit status
49: In i.p(...) :
  installation of package ‘/tmp/RtmpQE2e9e/file36a2744704520/echofinemap_0.99.3.tar.gz’ had non-zero exit status
50: In i.p(...) : installation of package ‘XML’ had non-zero exit status

Session info

R version 4.1.3 (2022-03-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux 8.6 (Ootpa)

Matrix products: default
BLAS/LAPACK: /autofs/nccs-svm1_home1/anuragv/.conda/envs/echoverse/lib/libopenblasp-r0.3.21.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] remotes_2.4.2

loaded via a namespace (and not attached):
[1] compiler_4.1.3 tools_4.1.3    curl_4.3.2

Thank you!

vermaa1 commented 1 year ago

After some more troubleshooting, I found the issue was with the missing libxml library. After installing the library (conda install r-xml), echolocatoR installation finished successfully!

bschilder commented 1 year ago

Ah yes, XML is a tricky R dep to install on some machines. I'll add a note about this in the troubleshooting section of the README.

Thanks for reporting this!

bschilder commented 1 year ago

Done! https://github.com/RajLabMSSM/echolocatoR#installation-troubleshooting