HenrikBengtsson/matrixStats

HELP ME WITH colmaxs in R

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Dianabeth3 commented

Good morning, how are you?
I am running poolparty but in the PPstat module, I get the following error:

le$ bash PPstats pp_stats.config |& tee log.stats_example.txt
ALERT: pp_stats.config has been specified as the configuration file
[1] "R ALERT: Checking for R dependencies. Will attempt to install automatically if not present."
CONF: Parameter check passed. moving on...
CONF 1/8 Complete, summary acquired and proportion of genomic overlap detected
CONF 2/8 Complete, total mean coverage calculated
CONF 3/8 Complete, filtered mean coverage calculated
CONF 4/8 Complete, proportion of ref genome calculated
CONF 5/8 Complete, scaffold proportion calculated
CONF 6/8 Complete, anchored proportion calculated
CONF 7/8 Complete, interval proportion calculated
CONF 8/8 Complete, chromosome proportion calculated
CONF BASH portion of run is complete
CONF Loading R to plot results and create tables
[1] "R ALERT: Summary Written"
Error in colMaxs(tma$Mean_Coverage) : could not find function "colMaxs"
Execution halted
CONF all files have been written to /home/ecolintegr/bin/poolparty/example/stats
(poolparty_env) ecolintegr@ecolintegr-Precision-5820-Tower:~/bin/poolparty/example$

I installed the rpm package, but it does not generate the output pdf files. Could you help me or what should I do, I installed R 4.0.0.

Saludos,
Diana

HenrikBengtsson commented

Hello, please reach out to the maintainer of PPstats for help, who need to make sure the matrixStats package is loaded.

Dianabeth3 commented