##############################################################################
Pathview is an open source software package distributed under GNU General
Public License version 3 (GPLv3). Details of GPLv3 is available at
http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
formally cite the original Pathview paper (not just mention it) in publications
or products. For details, do citation("pathview") within R.
The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
license agreement (details at http://www.kegg.jp/kegg/legal.html).
##############################################################################
Failed to create bus connection: No such file or directory
── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
✔ dplyr 1.1.4 ✔ readr 2.1.4
✔ forcats 1.0.0 ✔ stringr 1.5.1
✔ ggplot2 3.4.4 ✔ tibble 3.2.1
✔ lubridate 1.9.3 ✔ tidyr 1.3.0
✔ purrr 1.0.2
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag() masks stats::lag()
ℹ Use the conflicted package () to force all conflicts to become errors
Warning message:
In system("timedatectl", intern = TRUE) :
running command 'timedatectl' had status 1
Warning messages:
1: Using an external vector in selections was deprecated in tidyselect 1.1.0.
ℹ Please use `all_of()` or `any_of()` instead.
# Was:
data %>% select(category)
# Now:
data %>% select(all_of(category))
See .
2: There were 2 warnings in `summarise()`.
The first warning was:
ℹ In argument: `Row.names = (function (x, ...) ...`.
ℹ In group 1: `group = "Group1"`.
Caused by warning in `mean.default()`:
! argument is not numeric or logical: returning NA
ℹ Run `dplyr::last_dplyr_warnings()` to see the 1 remaining warning.
3: There were 2 warnings in `summarise()`.
The first warning was:
ℹ In argument: `Row.names = (function (x, ...) ...`.
ℹ In group 1: `group = "Group1"`.
Caused by warning in `mean.default()`:
! argument is not numeric or logical: returning NA
ℹ Run `dplyr::last_dplyr_warnings()` to see the 1 remaining warning.
'select()' returned 1:1 mapping between keys and columns
Warning: None of the genes or compounds mapped to the pathway!
Argument gene.idtype or cpd.idtype may be wrong.
Info: Working in directory /var/www/cloud_workdir/pipelines/976/trancriptomics_and_metabolomics_kD8XhvoWpxhRCcn2ekesMu/one_stepNeA8VjPhyuR6BUFqNJdTMk_result/Report/customer_files/05_联合通路图
Info: Writing image file hsa02010..multi.png
'select()' returned 1:1 mapping between keys and columns
Warning: None of the genes or compounds mapped to the pathway!
Argument gene.idtype or cpd.idtype may be wrong.
Info: Working in directory /var/www/cloud_workdir/pipelines/976/trancriptomics_and_metabolomics_kD8XhvoWpxhRCcn2ekesMu/one_stepNeA8VjPhyuR6BUFqNJdTMk_result/Report/customer_files/05_联合通路图
Info: Writing image file hsa04210..multi.png
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /var/www/cloud_workdir/pipelines/976/trancriptomics_and_metabolomics_kD8XhvoWpxhRCcn2ekesMu/one_stepNeA8VjPhyuR6BUFqNJdTMk_result/Report/customer_files/05_联合通路图
Info: Writing image file hsa04514..multi.png
Warning: None of the genes or compounds mapped to the pathway!
Argument gene.idtype or cpd.idtype may be wrong.
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /var/www/cloud_workdir/pipelines/976/trancriptomics_and_metabolomics_kD8XhvoWpxhRCcn2ekesMu/one_stepNeA8VjPhyuR6BUFqNJdTMk_result/Report/customer_files/05_联合通路图
Info: Writing image file hsa00591..multi.png
Warning: None of the genes or compounds mapped to the pathway!
Argument gene.idtype or cpd.idtype may be wrong.
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /var/www/cloud_workdir/pipelines/976/trancriptomics_and_metabolomics_kD8XhvoWpxhRCcn2ekesMu/one_stepNeA8VjPhyuR6BUFqNJdTMk_result/Report/customer_files/05_联合通路图
Info: Writing image file hsa00590..multi.png
Warning messages:
1: In colnames(plot.data)[c(1, 3, 9:ncs)] <- c("kegg.names", "all.mapped", :
number of items to replace is not a multiple of replacement length
2: In colnames(plot.data)[c(1, 3, 9:ncs)] <- c("kegg.names", "all.mapped", :
number of items to replace is not a multiple of replacement length
3: In colnames(plot.data)[c(1, 3, 9:ncs)] <- c("kegg.names", "all.mapped", :
number of items to replace is not a multiple of replacement length
4: In colnames(plot.data)[c(1, 3, 9:ncs)] <- c("kegg.names", "all.mapped", :
number of items to replace is not a multiple of replacement length