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License: Other
Finding an Active Metabolic Module in Atom Transition Network
License: Other
Option for makeAtomGraph
Function should check, whether sgmwcs binary exists and can be run. Otherwise the run results in cryptic error.
Add map from formula for kegg.met.db
Hi,
when trying to instal the package with devtools::install_github("ctlab/gatom")
, I get the following error:
* installing *source* package ‘gatom’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** tests
** byte-compile and prepare package for lazy loading
Error : object ‘is_vector_s3’ is not exported by 'namespace:tibble'
I have both sgmwcs solver and cplex solver in PATH, and here's session info:
R version 3.5.0 (2018-04-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.2 (Nitrogen)
Matrix products: default
BLAS/LAPACK: /nfs/software/as/el7.2/EasyBuild/CRG/software/OpenBLAS/0.2.20-GCC-6.4.0-2.28/lib/libopenblas_sandybridgep-r0.2.20.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
loaded via a namespace (and not attached):
[1] httr_1.3.1 compiler_3.5.0 R6_2.4.1
[4] BiocInstaller_1.30.0 tools_3.5.0 withr_2.2.0
[7] curl_3.1 memoise_1.1.0 knitr_1.20
[10] git2r_0.21.0 digest_0.6.25 devtools_1.13.5
Any suggestions what could be wrong?
Thanks in advance,
Anamaria
Hello. I try open network in Cytoscape (v. 3.5.1), but I receive error "Could not parse XGMML file" (in svg everything is fine).
Could you give me some advice how solve the problem?
Using repel-like algorithm
Zero p-values should be replaced with some epsilng with a warning.
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