seq2pathway error on Mac OS X
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termanini ▴ 10
@termanini-8493
Last seen 5.0 years ago

Hello, I am trying the seq2pathway package under Mac OS X.

As requested I have python2.7 installed.

However, I got an error when running the function runseq2gene(): 

sh: C:/Python27/python: No such file or directory
Error in system(command, intern = TRUE) : error in running command

It seems that under Mac OS X the package is searching for python thinking that it is running under Windows OS instead of OS X.

Best,
Alberto

---

> sessionInfo();

R version 3.2.2 (2015-08-14)

Platform: x86_64-apple-darwin13.4.0 (64-bit)

Running under: OS X 10.10.3 (Yosemite)

 

locale:

[1] it_IT.UTF-8/it_IT.UTF-8/it_IT.UTF-8/C/en_US.UTF-8/it_IT.UTF-8

 

attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base     

 

other attached packages:

[1] seq2pathway_1.0.0 RSQLite_1.0.0     DBI_0.3.1        

 

loaded via a namespace (and not attached):

 [1] fastcluster_1.1.16     reshape2_1.4.1         splines_3.2.2         

 [4] lattice_0.20-33        colorspace_1.2-6       stats4_3.2.2          

 [7] survival_2.38-3        XML_3.98-1.3           foreign_0.8-66        

[10] BiocGenerics_0.14.0    RColorBrewer_1.1-2     matrixStats_0.14.2    

[13] foreach_1.4.2          plyr_1.8.3             GSA_1.03              

[16] stringr_1.0.0          munsell_0.4.2          gtable_0.1.2          

[19] codetools_0.2-14       seq2pathway.data_1.0.0 latticeExtra_0.6-26   

[22] Biobase_2.28.0         IRanges_2.2.7          biomaRt_2.24.1        

[25] doParallel_1.0.8       GenomeInfoDb_1.4.2     parallel_3.2.2        

[28] AnnotationDbi_1.30.1   preprocessCore_1.30.0  proto_0.3-10          

[31] Rcpp_0.12.1            acepack_1.3-3.3        scales_0.3.0          

[34] S4Vectors_0.6.5        Hmisc_3.16-0           WGCNA_1.47            

[37] XVector_0.8.0          gridExtra_2.0.0        impute_1.42.0         

[40] ggplot2_1.0.1          digest_0.6.8           stringi_0.5-5         

[43] GenomicRanges_1.20.6   grid_3.2.2             tools_3.2.2           

[46] bitops_1.0-6           magrittr_1.5           RCurl_1.95-4.7        

[49] dynamicTreeCut_1.62    Formula_1.2-1          cluster_2.0.3         

[52] GO.db_3.1.2            MASS_7.3-44            reshape_0.8.5         

[55] iterators_1.0.7        rpart_4.1-10           nnet_7.3-11           

 

 

seq2pathway error python mac os x • 918 views
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1
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@valerie-obenchain-4275
Last seen 21 months ago
United States

The package maintainer has been notified about this problem. They have not yet updated their package and in the interim it has been marked as 'deprecated' in the devel branch.

Valerie

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Entering edit mode
Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 5 months ago
China/Guangzhou/Southern Medical Univer…

known issue, see seq2pathway is not platform-independent

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Entering edit mode
Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 5 months ago
China/Guangzhou/Southern Medical Univer…

the author has fixed this issue in version >=1.1.6, see his comment in http://ygc.name/2015/08/21/functional-enrichment-analysis-with-ngs-data/#comment-19209

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Entering edit mode
termanini ▴ 10
@termanini-8493
Last seen 5.0 years ago

Thanks guys!

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