diff --git a/revdep/README.md b/revdep/README.md index 19655ec..5ab5cb7 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -10,33 +10,33 @@ |collate |en_US.UTF-8 | |ctype |en_US.UTF-8 | |tz |America/Los_Angeles | -|date |2024-12-15 | +|date |2025-01-29 | |pandoc |3.6 @ /software/c4/cbi/software/pandoc-3.6/bin/pandoc | # Dependencies |package |old |new |Δ | |:----------|:------|:-----------|:--| -|parallelly |1.40.1 |1.40.1-9007 |* | +|parallelly |1.41.0 |1.41.0-9011 |* | # Revdeps -## All (60) +## All (63) |package |version |error |warning |note | |:-------------------|:-------|:-----|:-------|:----| |[adea](problems.md#adea)|1.5.2 |1 | | | |alookr |0.3.9 | | | | -|amadeus |1.1.6 | | | | +|bbw |0.3.0 | | | | |bigparallelr |0.3.2 | | | | |bigreadr |0.2.5 | | | | |[bootUR](problems.md#bootur)|1.0.4 | | |2 | -|[breathteststan](problems.md#breathteststan)|0.8.8 | | |2 | +|[breathteststan](problems.md#breathteststan)|0.8.9 | | |2 | |cccrm |3.0.3 | | | | -|[COTAN](problems.md#cotan)|2.6.1 | | |3 | +|[COTAN](problems.md#cotan)|2.6.2 | | |3 | |CptNonPar |0.2.1 | | | | |dataquieR |2.1.0 | | | | -|[decoupleR](problems.md#decoupler)|2.12.0 | |1 |1 | +|[decoupleR](problems.md#decoupler)|2.12.0 |3 |1 |1 | |DEoptim |2.2-8 | | | | |[desla](problems.md#desla)|0.3.0 | | |1 | |fiery |1.2.1 | | | | @@ -45,12 +45,12 @@ |future |1.34.0 | | | | |future.batchtools |0.12.1 | | | | |future.mirai |0.2.2 | | | | -|[gastempt](problems.md#gastempt)|0.6.2 | | |2 | +|[gastempt](problems.md#gastempt)|0.7.0 | | |2 | |GREENeR |1.0.0 | | | | |greta |0.5.0 | | | | -|[gtfstools](problems.md#gtfstools)|1.3.0 | | |1 | +|[gtfstools](problems.md#gtfstools)|1.4.0 | | |1 | |IFAA |1.8.0 | | | | -|[InPAS](problems.md#inpas)|2.14.0 | |1 |2 | +|[InPAS](problems.md#inpas)|2.14.1 | |1 |2 | |[JMbayes2](problems.md#jmbayes2)|0.5-0 | | |1 | |kernelboot |0.1.10 | | | | |LWFBrook90R |0.6.1 | | | | @@ -59,25 +59,28 @@ |mlr3 |0.22.1 | | | | |[mmrm](problems.md#mmrm)|0.3.14 | | |1 | |modeltime |1.3.1 | | | | -|multilevelmediation |0.3.1 | | | | +|multilevelmediation |0.4.1 | | | | |[NCC](problems.md#ncc)|1.0 | | |1 | |[nebula](problems.md#nebula)|1.5.3 | | |1 | |[outliers.ts.oga](problems.md#outlierstsoga)|0.0.1 | |1 | | -|parseRPDR |1.1.1 | | | | +|parseRPDR |1.1.2 | | | | |[pmartR](problems.md#pmartr)|2.4.6 | | |2 | |proffer |0.2.2 | | | | |[QDNAseq](problems.md#qdnaseq)|1.42.0 | |1 | | |[qtl2pleio](problems.md#qtl2pleio)|1.4.3 | | |2 | +|rbiom |2.0.13 | | | | |[ResIN](problems.md#resin)|2.0.0 | | |1 | |rivnet |0.5.0 | | | | |Rtapas |1.2 | | | | |SCDB |0.4.1 | | | | |[scruff](problems.md#scruff)|1.24.0 | | |5 | +|seqimpute |2.2.0 | | | | |[SimDesign](problems.md#simdesign)|2.18 | | |1 | |simIDM |0.1.0 | | | | +|spanishoddata |0.1.0 | | | | |specr |1.0.0 | | | | -|[streetscape](problems.md#streetscape)|1.0.3 | |1 |1 | -|[targets](problems.md#targets)|1.9.1 | | |1 | +|[streetscape](problems.md#streetscape)|1.0.5 | |1 |1 | +|[targets](problems.md#targets)|1.10.0 | | |1 | |TaxaNorm |2.4 | | | | |[TDApplied](problems.md#tdapplied)|3.0.4 | | |1 | |tern.mmrm |0.3.2 | | | | diff --git a/revdep/cran.md b/revdep/cran.md index bc84568..0c050e9 100644 --- a/revdep/cran.md +++ b/revdep/cran.md @@ -1,6 +1,6 @@ ## revdepcheck results -We checked 60 reverse dependencies (54 from CRAN + 6 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. +We checked 63 reverse dependencies (57 from CRAN + 6 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. * We saw 0 new problems * We failed to check 0 packages diff --git a/revdep/problems.md b/revdep/problems.md index 1d4e852..9407dc5 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -40,9 +40,9 @@ Run `revdepcheck::revdep_details(, "bootUR")` for more info * checking installed package size ... NOTE ``` - installed size is 6.7Mb + installed size is 6.6Mb sub-directories of 1Mb or more: - libs 6.3Mb + libs 6.2Mb ``` * checking for GNU extensions in Makefiles ... NOTE @@ -54,10 +54,10 @@ Run `revdepcheck::revdep_details(, "bootUR")` for more info
-* Version: 0.8.8 +* Version: 0.8.9 * GitHub: https://github.com/dmenne/breathteststan * Source code: https://github.com/cran/breathteststan -* Date/Publication: 2024-12-03 16:10:02 UTC +* Date/Publication: 2025-01-08 09:00:07 UTC * Number of recursive dependencies: 152 Run `revdepcheck::revdep_details(, "breathteststan")` for more info @@ -68,9 +68,9 @@ Run `revdepcheck::revdep_details(, "breathteststan")` for more info * checking installed package size ... NOTE ``` - installed size is 64.3Mb + installed size is 64.0Mb sub-directories of 1Mb or more: - libs 64.0Mb + libs 63.7Mb ``` * checking for GNU extensions in Makefiles ... NOTE @@ -82,10 +82,10 @@ Run `revdepcheck::revdep_details(, "breathteststan")` for more info
-* Version: 2.6.1 +* Version: 2.6.2 * GitHub: https://github.com/seriph78/COTAN * Source code: https://github.com/cran/COTAN -* Date/Publication: 2024-11-12 +* Date/Publication: 2025-01-19 * Number of recursive dependencies: 276 Run `revdepcheck::revdep_details(, "COTAN")` for more info @@ -96,9 +96,9 @@ Run `revdepcheck::revdep_details(, "COTAN")` for more info * checking installed package size ... NOTE ``` - installed size is 13.7Mb + installed size is 13.6Mb sub-directories of 1Mb or more: - doc 11.9Mb + doc 11.8Mb ``` * checking dependencies in R code ... NOTE @@ -151,6 +151,79 @@ Run `revdepcheck::revdep_details(, "decoupleR")` for more info ## In both +* checking examples ... ERROR + ``` + Running examples in ‘decoupleR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: get_collectri + > ### Title: CollecTRI gene regulatory network. Wrapper to access CollecTRI + > ### gene regulatory network. CollecTRI is a comprehensive resource + > ### containing a curated collection of transcription factors (TFs) and + > ### their target genes. It is an expansion of DoRothEA. Each interaction + > ### is weighted by its mode of regulation (either positive or negative). + > ### Aliases: get_collectri + > + > ### ** Examples + > + > collectri <- get_collectri(organism='human', split_complexes=FALSE) + [2025-01-29 07:41:10] [WARN] [OmnipathR] Accessing `collectri` as a static table: this is not the recommended way to access OmniPath data; it is only a backup plan for situations when our server or your computer is experiencing issues. + Error in if (.keep) . else select(., -!!evs_col) : + argument is of length zero + Calls: get_collectri ... tidyselect_data_has_predicates -> unnest_evidences -> %>% + Execution halted + ``` + +* checking tests ... + ``` + Running ‘testthat.R’ + ERROR + Running the tests in ‘tests/testthat.R’ failed. + Last 50 lines of output: + 25. ├─OmnipathR:::has_column(., "evidences") + 26. │ ├─col %in% colnames(data) + 27. │ └─base::colnames(data) + 28. │ └─base::is.data.frame(x) + 29. ├─OmnipathR::filter_evidences(...) + 30. │ └─expr(...) %>% eval_select(data) %>% names %>% ... + ... + 25. ├─OmnipathR:::is_empty_2(.) + 26. │ └─value %>% ... + 27. ├─tidyselect::eval_select(., data) + 28. │ └─tidyselect::tidyselect_data_has_predicates(data) + 29. └─OmnipathR::unnest_evidences(., .keep = .keep) + 30. └─... %>% ... + + [ FAIL 5 | WARN 7 | SKIP 0 | PASS 29 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... ERROR + ``` + Error(s) in re-building vignettes: + --- re-building ‘decoupleR.Rmd’ using rmarkdown + [WARNING] Could not fetch resource https://github.com/saezlab/decoupleR/blob/master/inst/figures/net_plot.png?raw=1: HttpExceptionRequest Request { + host = "github.com" + port = 443 + secure = True + requestHeaders = [] + path = "/saezlab/decoupleR/blob/master/inst/figures/net_plot.png" + queryString = "?raw=1" + method = "GET" + ... + Quitting from lines 86-88 [collectri] (tf_sc.Rmd) + Error: processing vignette 'tf_sc.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘tf_sc.Rmd’ + + SUMMARY: processing the following files failed: + ‘tf_bk.Rmd’ ‘tf_sc.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + * checking Rd cross-references ... WARNING ``` Missing link or links in Rd file 'run_gsva.Rd': @@ -161,9 +234,9 @@ Run `revdepcheck::revdep_details(, "decoupleR")` for more info * checking installed package size ... NOTE ``` - installed size is 9.1Mb + installed size is 11.1Mb sub-directories of 1Mb or more: - doc 6.9Mb + doc 8.9Mb extdata 1.4Mb ``` @@ -194,10 +267,10 @@ Run `revdepcheck::revdep_details(, "desla")` for more info
-* Version: 0.6.2 +* Version: 0.7.0 * GitHub: https://github.com/dmenne/gastempt * Source code: https://github.com/cran/gastempt -* Date/Publication: 2024-12-04 07:50:02 UTC +* Date/Publication: 2024-12-20 07:50:02 UTC * Number of recursive dependencies: 109 Run `revdepcheck::revdep_details(, "gastempt")` for more info @@ -208,9 +281,9 @@ Run `revdepcheck::revdep_details(, "gastempt")` for more info * checking installed package size ... NOTE ``` - installed size is 177.2Mb + installed size is 176.3Mb sub-directories of 1Mb or more: - libs 176.7Mb + libs 175.8Mb ``` * checking for GNU extensions in Makefiles ... NOTE @@ -222,11 +295,11 @@ Run `revdepcheck::revdep_details(, "gastempt")` for more info
-* Version: 1.3.0 +* Version: 1.4.0 * GitHub: https://github.com/ipeaGIT/gtfstools * Source code: https://github.com/cran/gtfstools -* Date/Publication: 2024-10-07 18:40:02 UTC -* Number of recursive dependencies: 89 +* Date/Publication: 2025-01-09 00:40:02 UTC +* Number of recursive dependencies: 90 Run `revdepcheck::revdep_details(, "gtfstools")` for more info @@ -243,10 +316,10 @@ Run `revdepcheck::revdep_details(, "gtfstools")` for more info
-* Version: 2.14.0 +* Version: 2.14.1 * GitHub: NA * Source code: https://github.com/cran/InPAS -* Date/Publication: 2024-10-29 +* Date/Publication: 2024-12-23 * Number of recursive dependencies: 165 Run `revdepcheck::revdep_details(, "InPAS")` for more info @@ -296,7 +369,7 @@ Run `revdepcheck::revdep_details(, "InPAS")` for more info * GitHub: https://github.com/drizopoulos/JMbayes2 * Source code: https://github.com/cran/JMbayes2 * Date/Publication: 2024-05-30 07:30:03 UTC -* Number of recursive dependencies: 76 +* Number of recursive dependencies: 77 Run `revdepcheck::revdep_details(, "JMbayes2")` for more info @@ -351,9 +424,9 @@ Run `revdepcheck::revdep_details(, "mmrm")` for more info * checking installed package size ... NOTE ``` - installed size is 188.7Mb + installed size is 188.8Mb sub-directories of 1Mb or more: - libs 186.9Mb + libs 187.0Mb ``` # NCC @@ -364,7 +437,7 @@ Run `revdepcheck::revdep_details(, "mmrm")` for more info * GitHub: https://github.com/pavlakrotka/NCC * Source code: https://github.com/cran/NCC * Date/Publication: 2023-03-03 09:10:10 UTC -* Number of recursive dependencies: 113 +* Number of recursive dependencies: 116 Run `revdepcheck::revdep_details(, "NCC")` for more info @@ -623,10 +696,10 @@ Run `revdepcheck::revdep_details(, "SimDesign")` for more info
-* Version: 1.0.3 +* Version: 1.0.5 * GitHub: NA * Source code: https://github.com/cran/streetscape -* Date/Publication: 2024-08-31 06:10:02 UTC +* Date/Publication: 2025-01-21 14:50:03 UTC * Number of recursive dependencies: 139 Run `revdepcheck::revdep_details(, "streetscape")` for more info @@ -645,8 +718,8 @@ Run `revdepcheck::revdep_details(, "streetscape")` for more info code for methods in class “Rcpp_SpatExtent” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatFactor” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatFactor” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) - code for methods in class “Rcpp_SpatGraph” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) - code for methods in class “Rcpp_SpatGraph” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) + code for methods in class “Rcpp_SpatMessages” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) + code for methods in class “Rcpp_SpatMessages” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) ... code for methods in class “Rcpp_SpatVectorProxy” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatVectorProxy” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) @@ -670,8 +743,8 @@ Run `revdepcheck::revdep_details(, "streetscape")` for more info code for methods in class “Rcpp_SpatExtent” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatFactor” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpatFactor” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) - code for methods in class “Rcpp_SpatGraph” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) - code for methods in class “Rcpp_SpatGraph” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) + code for methods in class “Rcpp_SpatMessages” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) + code for methods in class “Rcpp_SpatMessages” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) ... code for methods in class “Rcpp_SpExtent” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) code for methods in class “Rcpp_SpPoly” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?) @@ -689,10 +762,10 @@ Run `revdepcheck::revdep_details(, "streetscape")` for more info
-* Version: 1.9.1 +* Version: 1.10.0 * GitHub: https://github.com/ropensci/targets * Source code: https://github.com/cran/targets -* Date/Publication: 2024-12-04 12:40:02 UTC +* Date/Publication: 2025-01-13 15:00:01 UTC * Number of recursive dependencies: 160 Run `revdepcheck::revdep_details(, "targets")` for more info