HenrikBengtsson
commented
1 year 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 1 year ago
HenrikBengtsson
commented
1 year ago Hello, please reach out to the maintainer of PPstats for help, who need to make sure the matrixStats package is loaded.
Dianabeth3
commented
1 year 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