Last updated on 2021-05-14 09:50:57 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.0 | 2.86 | 70.44 | 73.30 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.0.0 | 2.10 | 54.11 | 56.21 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.0.0 | 80.38 | WARN | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.0 | 76.28 | WARN | |||
| r-devel-windows-ix86+x86_64 | 1.0.0 | 6.00 | 79.00 | 85.00 | OK | |
| r-devel-windows-x86_64-gcc10-UCRT | 1.0.0 | WARN | ||||
| r-patched-linux-x86_64 | 1.0.0 | 3.16 | 68.26 | 71.42 | OK | |
| r-patched-solaris-x86 | 1.0.0 | 116.50 | OK | |||
| r-release-linux-x86_64 | 1.0.0 | 2.26 | 68.80 | 71.06 | OK | |
| r-release-macos-x86_64 | 1.0.0 | WARN | ||||
| r-release-windows-ix86+x86_64 | 1.0.0 | 4.00 | 102.00 | 106.00 | OK | |
| r-oldrel-macos-x86_64 | 1.0.0 | ERROR | ||||
| r-oldrel-windows-ix86+x86_64 | 1.0.0 | 4.00 | 50.00 | 54.00 | ERROR |
Version: 1.0.0
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘dittoSeq’
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64-gcc10-UCRT, r-release-macos-x86_64, r-oldrel-windows-ix86+x86_64
Version: 1.0.0
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘Download.Rmd’ using rmarkdown
CrulAdapter enabled!
HttrAdapter enabled!
net connect allowed
Quitting from lines 421-429 (Download.Rmd)
Error: processing vignette 'Download.Rmd' failed with diagnostics:
there is no package called 'dittoSeq'
--- failed re-building ‘Download.Rmd’
--- re-building ‘Upload.Rmd’ using rmarkdown
CrulAdapter enabled!
HttrAdapter enabled!
net connect allowed
ejecting cassette: Upload-vignette
CrulAdapter disabled!
HttrAdapter disabled!
net connect disabled
--- finished re-building ‘Upload.Rmd’
SUMMARY: processing the following file failed:
‘Download.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.0.0
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building 'Download.Rmd' using rmarkdown
CrulAdapter enabled!
HttrAdapter enabled!
net connect allowed
Quitting from lines 421-429 (Download.Rmd)
Error: processing vignette 'Download.Rmd' failed with diagnostics:
there is no package called 'dittoSeq'
--- failed re-building 'Download.Rmd'
--- re-building 'Upload.Rmd' using rmarkdown
CrulAdapter enabled!
HttrAdapter enabled!
net connect allowed
ejecting cassette: Upload-vignette
CrulAdapter disabled!
HttrAdapter disabled!
net connect disabled
--- finished re-building 'Upload.Rmd'
SUMMARY: processing the following file failed:
'Download.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-windows-x86_64-gcc10-UCRT
Version: 1.0.0
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘Download.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Bioconductor version '3.11' is out-of-date; the current release version '3.12'
is available with R version '4.0'; see https://bioconductor.org/install
CrulAdapter enabled!
HttrAdapter enabled!
net connect allowed
Quitting from lines 421-429 (Download.Rmd)
Error: processing vignette 'Download.Rmd' failed with diagnostics:
there is no package called 'dittoSeq'
--- failed re-building ‘Download.Rmd’
--- re-building ‘Upload.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Bioconductor version '3.11' is out-of-date; the current release version '3.12'
is available with R version '4.0'; see https://bioconductor.org/install
CrulAdapter enabled!
HttrAdapter enabled!
net connect allowed
ejecting cassette: Upload-vignette
CrulAdapter disabled!
HttrAdapter disabled!
net connect disabled
--- finished re-building ‘Upload.Rmd’
SUMMARY: processing the following file failed:
‘Download.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-macos-x86_64
Version: 1.0.0
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking: 'dittoSeq', 'BiocStyle'
Flavor: r-oldrel-macos-x86_64
Version: 1.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [5s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
Error: subscript out of bounds
Backtrace:
█
1. ├─vcr::use_cassette(...) test-update.R:10:0
2. │ └─cassette$call_block(...)
3. └─magmaR::retrieveMatrix(targ, "example", "rna_seq", "all", "gene_counts") test-update.R:11:4
4. └─base::lapply(...)
5. └─magmaR:::FUN(X[[i]], ...)
6. └─magmaR:::.matrix_retrieval_chunk(...)
7. └─base::lapply(...)
8. └─magmaR:::FUN(X[[i]], ...)
[ FAIL 5 | WARN 0 | SKIP 0 | PASS 29 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-macos-x86_64
Version: 1.0.0
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘Download.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 18-31 (Download.Rmd)
Error: processing vignette 'Download.Rmd' failed with diagnostics:
there is no package called 'BiocStyle'
--- failed re-building ‘Download.Rmd’
--- re-building ‘Upload.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 18-31 (Upload.Rmd)
Error: processing vignette 'Upload.Rmd' failed with diagnostics:
there is no package called 'BiocStyle'
--- failed re-building ‘Upload.Rmd’
SUMMARY: processing the following files failed:
‘Download.Rmd’ ‘Upload.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-macos-x86_64
Version: 1.0.0
Check: tests
Result: ERROR
Running 'testthat.R' [8s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library("testthat")
> test_check("magmaR")
Loading required package: magmaR
== Failed tests ================================================================
-- Error (test-matrix.R:14:9): retrieveMatrix ----------------------------------
Error: subscript out of bounds
Backtrace:
x
1. \-magmaR::retrieveMatrix(targ, "example", "rna_seq", attributeNames = "gene_counts") test-matrix.R:14:8
2. \-base::lapply(...)
3. \-magmaR:::FUN(X[[i]], ...)
4. \-magmaR:::.matrix_retrieval_chunk(...)
5. \-base::lapply(...)
6. \-magmaR:::FUN(X[[i]], ...)
-- Failure (test-matrix.R:41:9): retrieveMatrix warns but ignores empty records --
`mat` has type 'logical', not 'integer'.
-- Failure (test-matrix.R:42:9): retrieveMatrix warns but ignores empty records --
dim(mat) not equal to c(40, 12).
2/2 mismatches (average diff: 26)
[1] 0 - 40 == -40
[2] 0 - 12 == -12
-- Failure (test-special.R:26:3): retrieveIds ----------------------------------
`ret` has type 'integer', not 'character'.
-- Error (test-update.R:10:1): (code run outside of `test_that()`) -------------
Error: subscript out of bounds
Backtrace:
x
1. +-vcr::use_cassette(...) test-update.R:10:0
2. | \-cassette$call_block(...)
3. \-magmaR::retrieveMatrix(targ, "example", "rna_seq", "all", "gene_counts") test-update.R:11:4
4. \-base::lapply(...)
5. \-magmaR:::FUN(X[[i]], ...)
6. \-magmaR:::.matrix_retrieval_chunk(...)
7. \-base::lapply(...)
8. \-magmaR:::FUN(X[[i]], ...)
[ FAIL 5 | WARN 0 | SKIP 0 | PASS 29 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-windows-ix86+x86_64
Version: 1.0.0
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building 'Download.Rmd' using rmarkdown
Bioconductor version '3.10' is out-of-date; the current release version '3.12'
is available with R version '4.0'; see https://bioconductor.org/install
Quitting from lines 18-31 (Download.Rmd)
Error: processing vignette 'Download.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building 'Download.Rmd'
--- re-building 'Upload.Rmd' using rmarkdown
Bioconductor version '3.10' is out-of-date; the current release version '3.12'
is available with R version '4.0'; see https://bioconductor.org/install
Quitting from lines 18-31 (Upload.Rmd)
Error: processing vignette 'Upload.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building 'Upload.Rmd'
SUMMARY: processing the following files failed:
'Download.Rmd' 'Upload.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-windows-ix86+x86_64