Last updated on 2022-09-11 12:56:15 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.3.2 | 8.67 | 232.52 | 241.19 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 0.3.2 | 6.59 | 145.32 | 151.91 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 0.3.2 | 265.33 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 0.3.2 | 272.27 | NOTE | |||
| r-devel-windows-x86_64 | 0.3.2 | 30.00 | 228.00 | 258.00 | ERROR | |
| r-patched-linux-x86_64 | 0.3.2 | 12.78 | 194.97 | 207.75 | NOTE | |
| r-release-linux-x86_64 | 0.3.2 | 7.76 | 192.30 | 200.06 | NOTE | |
| r-release-macos-arm64 | 0.3.2 | 77.00 | NOTE | |||
| r-release-macos-x86_64 | 0.3.2 | 157.00 | NOTE | |||
| r-release-windows-x86_64 | 0.3.2 | 22.00 | 220.00 | 242.00 | ERROR | |
| r-oldrel-macos-arm64 | 0.3.2 | 133.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 0.3.2 | 140.00 | NOTE | |||
| r-oldrel-windows-ix86+x86_64 | 0.3.2 | 21.00 | 141.00 | 162.00 | WARN |
Version: 0.3.2
Check: LazyData
Result: NOTE
'LazyData' is specified without a 'data' directory
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64
Version: 0.3.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'case_study.Rmd' using rmarkdown
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.8.2 (2022-06-13 22:00:14 UTC) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.25.0 (2022-06-12 02:20:02 UTC) successfully loaded. See ?R.oo for help.
Attaching package: 'R.oo'
The following object is masked from 'package:R.methodsS3':
throw
The following objects are masked from 'package:methods':
getClasses, getMethods
The following objects are masked from 'package:base':
attach, detach, load, save
R.utils v2.12.0 (2022-06-28 03:20:05 UTC) successfully loaded. See ?R.utils for help.
Attaching package: 'R.utils'
The following object is masked from 'package:utils':
timestamp
The following objects are masked from 'package:base':
cat, commandArgs, getOption, isOpen, nullfile, parse, warnings
Attaching package: 'igraph'
The following object is masked from 'package:R.oo':
hierarchy
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:igraph':
normalize, path, union
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Attaching package: 'IRanges'
The following object is masked from 'package:R.oo':
trim
The following object is masked from 'package:grDevices':
windows
clusterProfiler v4.3.4 For help: https://yulab-smu.top/biomedical-knowledge-mining-book/
If you use clusterProfiler in published research, please cite:
T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo, and G Yu. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. The Innovation. 2021, 2(3):100141
Attaching package: 'clusterProfiler'
The following object is masked from 'package:AnnotationDbi':
select
The following object is masked from 'package:IRanges':
slice
The following object is masked from 'package:S4Vectors':
rename
The following object is masked from 'package:igraph':
simplify
The following object is masked from 'package:stats':
filter
trying URL 'https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393113/bin/pone.0122882.s001.xlsx'
Content type 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet' length 11004 bytes (10 KB)
==================================================
downloaded 10 KB
trying URL 'https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393113/bin/pone.0122882.s003.xls'
Content type 'application/vnd.ms-office' length 58880 bytes (57 KB)
==================================================
downloaded 57 KB
Picking joint bandwidth of 0.0412
Picking joint bandwidth of 0.0496
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
Warning in utils::download.file(url, quiet = TRUE, method = method, ...) :
URL 'https://rest.kegg.jp/link/hsa/pathway': status was 'Failure when receiving data from the peer'
Quitting from lines 240-254 (case_study.Rmd)
Error: processing vignette 'case_study.Rmd' failed with diagnostics:
Failed to download KEGG data. Wrong 'species' or the network is unreachable. The 'species' should be one of organisms listed in 'http://www.genome.jp/kegg/catalog/org_list.html'
--- failed re-building 'case_study.Rmd'
--- re-building 'using_cRegulome.Rmd' using rmarkdown
Picking joint bandwidth of 0.0445
--- finished re-building 'using_cRegulome.Rmd'
SUMMARY: processing the following file failed:
'case_study.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64
Version: 0.3.2
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building 'case_study.Rmd' using rmarkdown
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.8.2 (2022-06-13 22:00:14 UTC) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.25.0 (2022-06-12 02:20:02 UTC) successfully loaded. See ?R.oo for help.
Attaching package: 'R.oo'
The following object is masked from 'package:R.methodsS3':
throw
The following objects are masked from 'package:methods':
getClasses, getMethods
The following objects are masked from 'package:base':
attach, detach, load, save
R.utils v2.12.0 (2022-06-28 03:20:05 UTC) successfully loaded. See ?R.utils for help.
Attaching package: 'R.utils'
The following object is masked from 'package:utils':
timestamp
The following objects are masked from 'package:base':
cat, commandArgs, getOption, isOpen, nullfile, parse, warnings
Attaching package: 'igraph'
The following object is masked from 'package:R.oo':
hierarchy
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:igraph':
normalize, path, union
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Attaching package: 'IRanges'
The following object is masked from 'package:R.oo':
trim
The following object is masked from 'package:grDevices':
windows
clusterProfiler v4.2.2 For help: https://yulab-smu.top/biomedical-knowledge-mining-book/
If you use clusterProfiler in published research, please cite:
T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo, and G Yu. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. The Innovation. 2021, 2(3):100141
Attaching package: 'clusterProfiler'
The following object is masked from 'package:AnnotationDbi':
select
The following object is masked from 'package:IRanges':
slice
The following object is masked from 'package:S4Vectors':
rename
The following object is masked from 'package:igraph':
simplify
The following object is masked from 'package:stats':
filter
trying URL 'https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393113/bin/pone.0122882.s001.xlsx'
Warning in download.file("https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393113/bin/pone.0122882.s001.xlsx", :
InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Quitting from lines 44-55 (case_study.Rmd)
Error: processing vignette 'case_study.Rmd' failed with diagnostics:
cannot open URL 'https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393113/bin/pone.0122882.s001.xlsx'
--- failed re-building 'case_study.Rmd'
--- re-building 'using_cRegulome.Rmd' using rmarkdown
Picking joint bandwidth of 0.0445
--- finished re-building 'using_cRegulome.Rmd'
SUMMARY: processing the following file failed:
'case_study.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-windows-ix86+x86_64