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cjvanlissa / worcs

Rstudio project template and convenience functions for the Workflow for Open Reproducible Code in Science (WORCS)
https://cjvanlissa.github.io/worcs/
GNU General Public License v3.0
76 stars 11 forks source link

Create WORCS on an existing repository #121

Closed swvanderlaan closed 1 year ago

swvanderlaan commented 2 years ago

Hi,

I am using the code below to create the WORCS setup on an existing repository. 

worcs::worcs_project(
  path = ".", # the current folder
  manuscript = "none", # edit this if you want a manuscript
  preregistration = "COS", # edit this if you want a preregistration
  add_license = "CC_BY-NC-ND_4.0",
  use_renv = TRUE,
  remote_repo = "git@github.com:swvanderlaan/ELSIE.git", # add git repo
  verbose = TRUE
)

I am getting the messages below. How can I fix this error?

Thanks!

Sander

v  Initializing 'Git' repository.
v  Writing '.worcs' file.
v  Copying standard files.
v  Creating preregistration files.
v  Writing license file.
* Initializing project ...
* Discovering package dependencies ... Done!
* Copying packages into the cache ... [272/272] Done!
* Resolving missing dependencies  ... 
Retrieving 'https://cran.rstudio.com/bin/macosx/contrib/4.1/sjPlot_2.8.10.tgz' ...
    OK [downloaded 1.4 Mb in 0.2 secs]
Retrieving 'https://cran.rstudio.com/bin/macosx/contrib/4.1/bayestestR_0.11.5.tgz' ...
    OK [downloaded 3 Mb in 0.4 secs]
Retrieving 'https://cran.rstudio.com/bin/macosx/contrib/4.1/insight_0.15.0.tgz' ...
    OK [downloaded 1.7 Mb in 0.3 secs]
Retrieving 'https://cran.rstudio.com/bin/macosx/contrib/4.1/datawizard_0.2.3.tgz' ...
    OK [downloaded 1.4 Mb in 0.2 secs]
Retrieving 'https://cran.rstudio.com/bin/macosx/contrib/4.1/dplyr_1.0.8.tgz' ...
    OK [downloaded 1.2 Mb in 0.2 secs]
Retrieving 'https://cran.rstudio.com/bin/macosx/contrib/4.1/generics_0.1.2.tgz' ...
    OK [downloaded 75.2 Kb in 0.1 secs]
Retrieving 'https://cran.rstudio.com/bin/macosx/contrib/4.1/glue_1.6.1.tgz' ...
    OK [downloaded 148.6 Kb in 0.1 secs]
Retrieving 'https://cran.rstudio.com/bin/macosx/contrib/4.1/magrittr_2.0.2.tgz' ...
    OK [downloaded 222 Kb in 0.1 secs]
Retrieving 'https://cran.rstudio.com/bin/macosx/contrib/4.1/effectsize_0.6.0.1.tgz' ...
    OK [downloaded 648.1 Kb in 0.1 secs]
Retrieving 'https://cran.rstudio.com/bin/macosx/contrib/4.1/parameters_0.16.0.tgz' ...
    OK [downloaded 1.6 Mb in 0.4 secs]
Retrieving 'https://cran.rstudio.com/bin/macosx/contrib/4.1/performance_0.8.0.tgz' ...
    OK [downloaded 2.6 Mb in 0.8 secs]
Retrieving 'https://cran.rstudio.com/bin/macosx/contrib/4.1/MASS_7.3-55.tgz' ...
    OK [downloaded 1.1 Mb in 0.4 secs]
Retrieving 'https://cran.rstudio.com/bin/macosx/contrib/4.1/nlme_3.1-155.tgz' ...
    OK [downloaded 2.3 Mb in 0.3 secs]
Retrieving 'https://cran.rstudio.com/bin/macosx/contrib/4.1/yaml_2.2.2.tgz' ...
    OK [downloaded 198.4 Kb in 0.1 secs]
Retrieving 'https://cran.rstudio.com/bin/macosx/contrib/4.1/sjmisc_2.8.9.tgz' ...
    OK [downloaded 522.4 Kb in 0.3 secs]
Retrieving 'https://cran.rstudio.com/bin/macosx/contrib/4.1/broom_0.7.12.tgz' ...
    OK [downloaded 1.7 Mb in 0.5 secs]
Retrieving 'https://cran.rstudio.com/bin/macosx/contrib/4.1/tidyr_1.2.0.tgz' ...
    OK [downloaded 978.1 Kb in 0.3 secs]
Retrieving 'https://cran.rstudio.com/bin/macosx/contrib/4.1/emmeans_1.7.2.tgz' ...
    OK [downloaded 1.9 Mb in 0.5 secs]
Retrieving 'https://cran.rstudio.com/bin/macosx/contrib/4.1/mvtnorm_1.1-3.tgz' ...
    OK [downloaded 254.2 Kb in 0.1 secs]
Retrieving 'https://cran.rstudio.com/bin/macosx/contrib/4.1/lme4_1.1-28.tgz' ...
    OK [downloaded 7 Mb in 1.1 secs]
Retrieving 'https://cran.rstudio.com/bin/macosx/contrib/4.1/Rcpp_1.0.8.tgz' ...
    OK [downloaded 3.1 Mb in 0.9 secs]
Retrieving 'https://cran.rstudio.com/bin/macosx/contrib/4.1/nloptr_2.0.0.tgz' ...
    OK [downloaded 1.9 Mb in 0.4 secs]
Retrieving 'https://cran.rstudio.com/bin/macosx/contrib/4.1/testthat_3.1.2.tgz' ...
    OK [downloaded 2.8 Mb in 0.4 secs]
Retrieving 'https://cran.rstudio.com/bin/macosx/contrib/4.1/jsonlite_1.7.3.tgz' ...
    OK [downloaded 1.1 Mb in 0.2 secs]
Installing insight [0.15.0] ...
    OK [installed binary]
Moving insight [0.15.0] into the cache ...
    OK [moved to cache in 1 milliseconds]
Installing datawizard [0.2.3] ...
    OK [installed binary]
Moving datawizard [0.2.3] into the cache ...
    OK [moved to cache in 0.6 milliseconds]
Installing bayestestR [0.11.5] ...
    OK [installed binary]
Moving bayestestR [0.11.5] into the cache ...
    OK [moved to cache in 1 milliseconds]
Installing generics [0.1.2] ...
    OK [installed binary]
Moving generics [0.1.2] into the cache ...
    OK [moved to cache in 1.2 milliseconds]
Installing glue [1.6.1] ...
    OK [installed binary]
Moving glue [1.6.1] into the cache ...
    OK [moved to cache in 1 milliseconds]
Installing rlang [1.0.1] ...
    OK [linked cache]
Installing magrittr [2.0.2] ...
    OK [installed binary]
Moving magrittr [2.0.2] into the cache ...
    OK [moved to cache in 0.61 milliseconds]
Installing fansi [1.0.2] ...
    OK [linked cache]
Installing cli [3.2.0] ...
    OK [linked cache]
Installing crayon [1.5.0] ...
    OK [linked cache]
Installing pillar [1.7.0] ...
    OK [linked cache]
Installing dplyr [1.0.8] ...
    OK [installed binary]
Moving dplyr [1.0.8] into the cache ...
    OK [moved to cache in 1.5 milliseconds]
Installing parameters [0.16.0] ...
    OK [installed binary]
Moving parameters [0.16.0] into the cache ...
    OK [moved to cache in 0.59 milliseconds]
Installing performance [0.8.0] ...
    OK [installed binary]
Moving performance [0.8.0] into the cache ...
    OK [moved to cache in 0.76 milliseconds]
Installing effectsize [0.6.0.1] ...
    OK [installed binary]
Moving effectsize [0.6.0.1] into the cache ...
    OK [moved to cache in 0.68 milliseconds]
Installing MASS [7.3-55] ...
    OK [installed binary]
Moving MASS [7.3-55] into the cache ...
    OK [moved to cache in 0.66 milliseconds]
Installing sjlabelled [1.1.8] ...
    OK [linked cache]
Installing ggeffects [1.1.1] ...
    OK [linked cache]
Installing nlme [3.1-155] ...
    OK [installed binary]
Moving nlme [3.1-155] into the cache ...
    OK [moved to cache in 1.4 milliseconds]
Installing yaml [2.2.2] ...
    OK [installed binary]
Moving yaml [2.2.2] into the cache ...
    OK [moved to cache in 0.65 milliseconds]
Installing sjmisc [2.8.9] ...
    OK [installed binary]
Moving sjmisc [2.8.9] into the cache ...
    OK [moved to cache in 0.77 milliseconds]
Installing tidyr [1.2.0] ...
    OK [installed binary]
Moving tidyr [1.2.0] into the cache ...
    OK [moved to cache in 0.79 milliseconds]
Installing broom [0.7.12] ...
    OK [installed binary]
Moving broom [0.7.12] into the cache ...
    OK [moved to cache in 1.7 milliseconds]
Installing estimability [1.3] ...
    OK [linked cache]
Installing mvtnorm [1.1-3] ...
    OK [installed binary]
Moving mvtnorm [1.1-3] into the cache ...
    OK [moved to cache in 0.65 milliseconds]
Installing emmeans [1.7.2] ...
    OK [installed binary]
Moving emmeans [1.7.2] into the cache ...
    OK [moved to cache in 1.3 milliseconds]
Installing Rcpp [1.0.8] ...
    OK [installed binary]
Moving Rcpp [1.0.8] into the cache ...
    OK [moved to cache in 0.62 milliseconds]
Installing jsonlite [1.7.3] ...
    OK [installed binary]
Moving jsonlite [1.7.3] into the cache ...
    OK [moved to cache in 0.83 milliseconds]
Installing testthat [3.1.2] ...
    OK [installed binary]
Moving testthat [3.1.2] into the cache ...
    OK [moved to cache in 0.94 milliseconds]
Installing nloptr [2.0.0] ...
    OK [installed binary]
Moving nloptr [2.0.0] into the cache ...
    OK [moved to cache in 1.7 milliseconds]
Installing lme4 [1.1-28] ...
    OK [installed binary]
Moving lme4 [1.1-28] into the cache ...
    OK [moved to cache in 0.6 milliseconds]
Installing modelr [0.1.8] ...
    OK [linked cache]
Installing sjstats [0.18.1] ...
    OK [linked cache]
Installing sjPlot [2.8.10] ...
    OK [installed binary]
Moving sjPlot [2.8.10] into the cache ...
    OK [moved to cache in 1.1 milliseconds]
The following package(s) will be updated in the lockfile:

# Bioconductor =======================
- AnnotationDbi                       [* -> 1.56.2]
- AnnotationFilter                    [* -> 1.18.0]
- BSgenome                            [* -> 1.62.0]
- Biobase                             [* -> 2.54.0]
- BiocFileCache                       [* -> 2.2.0]
- BiocGenerics                        [* -> 0.40.0]
- BiocIO                              [* -> 1.4.0]
- BiocParallel                        [* -> 1.28.3]
- Biostrings                          [* -> 2.62.0]
- DelayedArray                        [* -> 0.20.0]
- DelayedMatrixStats                  [* -> 1.16.0]
- FDb.InfiniumMethylation.hg19        [* -> 2.2.0]
- GEOquery                            [* -> 2.62.1]
- GenomeInfoDb                        [* -> 1.30.0]
- GenomeInfoDbData                    [* -> 1.2.7]
- GenomicAlignments                   [* -> 1.30.0]
- GenomicFeatures                     [* -> 1.46.3]
- GenomicRanges                       [* -> 1.46.1]
- HDF5Array                           [* -> 1.22.1]
- IRanges                             [* -> 2.28.0]
- KEGGREST                            [* -> 1.34.0]
- MatrixGenerics                      [* -> 1.6.0]
- MultiAssayExperiment                [* -> 1.20.0]
- ProtGenerics                        [* -> 1.26.0]
- RaggedExperiment                    [* -> 1.18.0]
- Rhdf5lib                            [* -> 1.16.0]
- Rhtslib                             [* -> 1.26.0]
- Rsamtools                           [* -> 2.10.0]
- S4Vectors                           [* -> 0.32.3]
- SummarizedExperiment                [* -> 1.24.0]
- TxDb.Hsapiens.UCSC.hg19.knownGene   [* -> 3.2.2]
- VariantAnnotation                   [* -> 1.40.0]
- XVector                             [* -> 0.34.0]
- annotate                            [* -> 1.72.0]
- biomaRt                             [* -> 2.50.2]
- bumphunter                          [* -> 1.36.0]
- ensembldb                           [* -> 2.18.2]
- genefilter                          [* -> 1.76.0]
- illuminaio                          [* -> 0.36.0]
- limma                               [* -> 3.50.0]
- minfi                               [* -> 1.40.0]
- multtest                            [* -> 2.50.0]
- org.Hs.eg.db                        [* -> 3.14.0]
- preprocessCore                      [* -> 1.56.0]
- rhdf5                               [* -> 2.38.0]
- rhdf5filters                        [* -> 1.6.0]
- rtracklayer                         [* -> 1.54.0]
- siggenes                            [* -> 1.68.0]
- sparseMatrixStats                   [* -> 1.6.0]
- zlibbioc                            [* -> 1.40.0]

# CRAN ===============================
- BH                                  [* -> 1.78.0-0]
- BiocManager                         [* -> 1.30.16]
- CMplot                              [* -> 4.0.0]
- DBI                                 [* -> 1.1.2]
- DT                                  [* -> 0.20]
- KernSmooth                          [* -> 2.23-20]
- MASS                                [* -> 7.3-55]
- Matrix                              [* -> 1.4-0]
- MatrixModels                        [* -> 0.5-0]
- ModelMetrics                        [* -> 1.2.2.2]
- R.methodsS3                         [* -> 1.8.1]
- R.oo                                [* -> 1.24.0]
- R.utils                             [* -> 2.11.0]
- R6                                  [* -> 2.5.1]
- RColorBrewer                        [* -> 1.1-2]
- RCurl                               [* -> 1.98-1.5]
- RPostgreSQL                         [* -> 0.7-3]
- RSQLite                             [* -> 2.2.9]
- Rcpp                                [* -> 1.0.8]
- RcppArmadillo                       [* -> 0.10.7.5.0]
- RcppEigen                           [* -> 0.3.3.9.1]
- SQUAREM                             [* -> 2021.1]
- SparseM                             [* -> 1.81]
- UpSetR                              [* -> 1.4.0]
- XML                                 [* -> 3.99-0.8]
- abind                               [* -> 1.4-5]
- askpass                             [* -> 1.1]
- assertthat                          [* -> 0.2.1]
- backports                           [* -> 1.4.1]
- base64                              [* -> 2.0]
- base64enc                           [* -> 0.1-3]
- bayestestR                          [* -> 0.11.5]
- beanplot                            [* -> 1.2]
- bit                                 [* -> 4.0.4]
- bit64                               [* -> 4.0.5]
- bitops                              [* -> 1.0-7]
- blob                                [* -> 1.2.2]
- boot                                [* -> 1.3-28]
- brew                                [* -> 1.0-6]
- brio                                [* -> 1.1.3]
- broom                               [* -> 0.7.12]
- cachem                              [* -> 1.0.6]
- callr                               [* -> 3.7.0]
- car                                 [* -> 3.0-12]
- carData                             [* -> 3.0-5]
- caret                               [* -> 6.0-90]
- class                               [* -> 7.3-19]
- cli                                 [* -> 3.2.0]
- clipr                               [* -> 0.7.1]
- codetools                           [* -> 0.2-18]
- colorspace                          [* -> 2.0-2]
- commonmark                          [* -> 1.7]
- conquer                             [* -> 1.2.1]
- corrplot                            [* -> 0.92]
- cowplot                             [* -> 1.1.1]
- cpp11                               [* -> 0.4.2]
- crayon                              [* -> 1.5.0]
- credentials                         [* -> 1.3.2]
- crosstalk                           [* -> 1.2.0]
- curl                                [* -> 4.3.2]
- data.table                          [* -> 1.14.2]
- datawizard                          [* -> 0.2.3]
- dbplyr                              [* -> 2.1.1]
- desc                                [* -> 1.4.0]
- devtools                            [* -> 2.4.3]
- diffobj                             [* -> 0.3.5]
- digest                              [* -> 0.6.29]
- doRNG                               [* -> 1.8.2]
- dplyr                               [* -> 1.0.8]
- e1071                               [* -> 1.7-9]
- effectsize                          [* -> 0.6.0.1]
- ellipsis                            [* -> 0.3.2]
- emmeans                             [* -> 1.7.2]
- estimability                        [* -> 1.3]
- evaluate                            [* -> 0.14]
- fansi                               [* -> 1.0.2]
- farver                              [* -> 2.1.0]
- fastmap                             [* -> 1.1.0]
- filelock                            [* -> 1.0.2]
- forcats                             [* -> 0.5.1]
- foreach                             [* -> 1.5.1]
- foreign                             [* -> 0.8-81]
- formatR                             [* -> 1.11]
- fs                                  [* -> 1.5.2]
- futile.logger                       [* -> 1.4.3]
- futile.options                      [* -> 1.0.1]
- future                              [* -> 1.23.0]
- future.apply                        [* -> 1.8.1]
- gdata                               [* -> 2.18.0]
- generics                            [* -> 0.1.2]
- gert                                [* -> 1.5.0]
- ggeffects                           [* -> 1.1.1]
- ggplot2                             [* -> 3.3.5]
- ggpubr                              [* -> 0.4.0]
- ggrepel                             [* -> 0.9.1]
- ggsci                               [* -> 2.9]
- ggsignif                            [* -> 0.6.3]
- gh                                  [* -> 1.3.0]
- gitcreds                            [* -> 0.1.1]
- globals                             [* -> 0.14.0]
- glue                                [* -> 1.6.1]
- gower                               [* -> 0.2.2]
- gridExtra                           [* -> 2.3]
- gtable                              [* -> 0.3.0]
- gtools                              [* -> 3.9.2]
- haven                               [* -> 2.4.3]
- highr                               [* -> 0.9]
- hms                                 [* -> 1.1.1]
- htm2txt                             [* -> 2.1.1]
- htmltools                           [* -> 0.5.2]
- htmlwidgets                         [* -> 1.5.4]
- httr                                [* -> 1.4.2]
- ini                                 [* -> 0.3.1]
- insight                             [* -> 0.15.0]
- ipred                               [* -> 0.9-12]
- isoband                             [* -> 0.2.5]
- iterators                           [* -> 1.0.13]
- jquerylib                           [* -> 0.1.4]
- jsonlite                            [* -> 1.7.3]
- knitr                               [* -> 1.37]
- labeling                            [* -> 0.4.2]
- labelled                            [* -> 2.9.0]
- lambda.r                            [* -> 1.2.4]
- later                               [* -> 1.3.0]
- lattice                             [* -> 0.20-45]
- lava                                [* -> 1.6.10]
- lazyeval                            [* -> 0.2.2]
- lifecycle                           [* -> 1.0.1]
- listenv                             [* -> 0.8.0]
- lme4                                [* -> 1.1-28]
- locfit                              [* -> 1.5-9.4]
- lubridate                           [* -> 1.8.0]
- magrittr                            [* -> 2.0.2]
- maptools                            [* -> 1.1-2]
- matrixStats                         [* -> 0.61.0]
- mclust                              [* -> 5.4.9]
- memoise                             [* -> 2.0.1]
- mgcv                                [* -> 1.8-38]
- mime                                [* -> 0.12]
- minqa                               [* -> 1.2.4]
- modelr                              [* -> 0.1.8]
- munsell                             [* -> 0.5.0]
- mvtnorm                             [* -> 1.1-3]
- nlme                                [* -> 3.1-155]
- nloptr                              [* -> 2.0.0]
- nnet                                [* -> 7.3-16]
- nor1mix                             [* -> 1.3-0]
- numDeriv                            [* -> 2016.8-1.1]
- openssl                             [* -> 1.4.6]
- openxlsx                            [* -> 4.2.5]
- pROC                                [* -> 1.18.0]
- parallelly                          [* -> 1.30.0]
- parameters                          [* -> 0.16.0]
- pbkrtest                            [* -> 0.5.1]
- performance                         [* -> 0.8.0]
- pillar                              [* -> 1.7.0]
- pkgbuild                            [* -> 1.3.1]
- pkgconfig                           [* -> 2.0.3]
- pkgload                             [* -> 1.2.4]
- plogr                               [* -> 0.2.0]
- pls                                 [* -> 2.8-0]
- plyr                                [* -> 1.8.6]
- png                                 [* -> 0.1-7]
- polynom                             [* -> 1.4-0]
- praise                              [* -> 1.0.0]
- prereg                              [* -> 0.5.0]
- prettyunits                         [* -> 1.1.1]
- processx                            [* -> 3.5.2]
- prodlim                             [* -> 2019.11.13]
- progress                            [* -> 1.2.2]
- progressr                           [* -> 0.10.0]
- promises                            [* -> 1.2.0.1]
- proxy                               [* -> 0.4-26]
- ps                                  [* -> 1.6.0]
- purrr                               [* -> 0.3.4]
- quadprog                            [* -> 1.5-8]
- quantreg                            [* -> 5.86]
- ranger                              [* -> 0.13.1]
- rappdirs                            [* -> 0.3.3]
- rcmdcheck                           [* -> 1.4.0]
- readr                               [* -> 2.1.1]
- recipes                             [* -> 0.1.17]
- rematch2                            [* -> 2.1.2]
- remotes                             [* -> 2.4.2]
- renv                                [* -> 0.15.0]
- reshape                             [* -> 0.8.8]
- reshape2                            [* -> 1.4.4]
- restfulr                            [* -> 0.0.13]
- rjson                               [* -> 0.2.21]
- rlang                               [* -> 1.0.1]
- rmarkdown                           [* -> 2.11]
- rngtools                            [* -> 1.5.2]
- roxygen2                            [* -> 7.1.2]
- rpart                               [* -> 4.1-15]
- rprojroot                           [* -> 2.0.2]
- rstatix                             [* -> 0.7.0]
- rstudioapi                          [* -> 0.13]
- rticles                             [* -> 0.22]
- rversions                           [* -> 2.1.1]
- scales                              [* -> 1.1.1]
- scrime                              [* -> 1.3.5]
- sessioninfo                         [* -> 1.2.2]
- sjPlot                              [* -> 2.8.10]
- sjlabelled                          [* -> 1.1.8]
- sjmisc                              [* -> 2.8.9]
- sjstats                             [* -> 0.18.1]
- snow                                [* -> 0.4-4]
- sp                                  [* -> 1.4-6]
- stringi                             [* -> 1.7.6]
- stringr                             [* -> 1.4.0]
- survival                            [* -> 3.2-13]
- sys                                 [* -> 3.4]
- testthat                            [* -> 3.1.2]
- tibble                              [* -> 3.1.6]
- tidyr                               [* -> 1.2.0]
- tidyselect                          [* -> 1.1.1]
- timeDate                            [* -> 3043.102]
- tinytex                             [* -> 0.36]
- tzdb                                [* -> 0.2.0]
- usethis                             [* -> 2.1.5]
- utf8                                [* -> 1.2.2]
- vctrs                               [* -> 0.3.8]
- viridisLite                         [* -> 0.4.0]
- vroom                               [* -> 1.5.7]
- waldo                               [* -> 0.3.1]
- whisker                             [* -> 0.4]
- withr                               [* -> 2.4.3]
- xfun                                [* -> 0.29]
- xml2                                [* -> 1.3.3]
- xopen                               [* -> 1.0.0]
- xtable                              [* -> 1.8-4]
- yaml                                [* -> 2.2.2]
- zip                                 [* -> 2.2.0]

# GitHub =============================
- BBMRIomics                          [* -> bbmri-nl/BBMRIomics:BBMRIomics@HEAD]
- DNAmArray                           [* -> molepi/DNAmArray@HEAD]
- omicsPrint                          [* -> molepi/omicsPrint@HEAD]
- patchwork                           [* -> thomasp85/patchwork@HEAD]
- worcs                               [* -> cjvanlissa/worcs@HEAD]

* Lockfile written to '~/git/swvanderlaan/ELSIE/renv.lock'.
v  Initializing 'renv' for a reproducible R environment.
Error in if (!after) c(values, x) else if (after >= lengx) c(x, values) else c(x[1L:after],  : 
  argument is of length zero
cjvanlissa commented 2 years ago

That does not look like a worcs error, I think it's an error in either renv or one of the packages; I see that tidyr had this error before (https://github.com/tidyverse/tidyr/issues/355). My advice would be to initialize the project without renv, and see if you can add renv using renv::init() once the project is set up!