HenrikBengtsson
commented
11 months ago Hello, please reach out to the maintainer of PPstats for help, who need to make sure the matrixStats package is loaded.
Closed Dianabeth3 closed 11 months ago
HenrikBengtsson
commented
11 months ago Hello, please reach out to the maintainer of PPstats for help, who need to make sure the matrixStats package is loaded.
Dianabeth3
commented
11 months ago Hello, I installed matrixStats but I have the same error
remotes::install_github("HenrikBengtsson/matrixStats", ref="develop")
remotes::install_github("HenrikBengtsson/matrixStats", ref="develop")
Downloading GitHub repo @.*** ── R CMD build ───────────────────────────────────────────────────────────────── checking for file ‘/tmp/RtmputjgmQ/remotes340bc3e161b4b/HenrikBengtsson-matri✔ checking for file ‘/tmp/RtmputjgmQ/remotes340bc3e161b4b/HenrikBengtsson-matrixStats-5122929/DESCRIPTION’ ─ preparing ‘matrixStats’: ✔ checking DESCRIPTION meta-information ... ─ cleaning src ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories ─ building ‘matrixStats_1.0.0-9002.tar.gz’
library(“matrixStats”)”) Error: unexpected input in "library(“" library("matrixStats") bash PPstats pp_stats.config |& tee log.stats_example.txt Error: unexpected symbol in "bash PPstats" bash PPstats pp_stats.config |& tee log.stats_example.txt Error: unexpected symbol in "bash PPstats" quit(save="no") (poolparty_env) @.:~/bin/poolparty/example$ 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$Mean_Coverage) : could not find function "colMaxs" Execution halted CONF all files have been written to /home/ecolintegr/bin/poolparty/example/stats (poolparty_env) @.:~/bin/poolparty/example$ c
El dom, 15 oct 2023 a las 23:47, Henrik Bengtsson @.***>) escribió:
Hello, please reach out to the maintainer of PPstats for help, who need to make sure the matrixStats package is loaded.
— Reply to this email directly, view it on GitHub https://github.com/HenrikBengtsson/matrixStats/issues/239#issuecomment-1763642152, or unsubscribe https://github.com/notifications/unsubscribe-auth/BDJJ6EE4UFLVHDDDHI2JM2TX7SN47ANCNFSM6AAAAAA6BNDMNE . You are receiving this because you authored the thread.Message ID: @.***>
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