Question: seq2pathway error on Mac OS X
0
gravatar for termanini
4.2 years ago by
termanini10
termanini10 wrote:

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           

 

 

ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by termanini10
Answer: seq2pathway error on Mac OS X
1
gravatar for Valerie Obenchain
4.2 years ago by
United States
Valerie Obenchain6.7k wrote:

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

ADD COMMENTlink written 4.2 years ago by Valerie Obenchain6.7k
Answer: seq2pathway error on Mac OS X
1
gravatar for Guangchuang Yu
4.2 years ago by
Guangchuang Yu1.1k
China/Guangzhou/Southern Medical University
Guangchuang Yu1.1k wrote:

known issue, see seq2pathway is not platform-independent

ADD COMMENTlink written 4.2 years ago by Guangchuang Yu1.1k
Answer: seq2pathway error on Mac OS X
1
gravatar for Guangchuang Yu
4.2 years ago by
Guangchuang Yu1.1k
China/Guangzhou/Southern Medical University
Guangchuang Yu1.1k wrote:

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

ADD COMMENTlink written 4.2 years ago by Guangchuang Yu1.1k
Answer: seq2pathway error on Mac OS X
0
gravatar for termanini
4.2 years ago by
termanini10
termanini10 wrote:

Thanks guys!

ADD COMMENTlink written 4.2 years ago by termanini10
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