Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Bioconductor installation issue for R 3.6.0 #573

Open
colearendt opened this issue Aug 23, 2019 · 12 comments
Open

Bioconductor installation issue for R 3.6.0 #573

colearendt opened this issue Aug 23, 2019 · 12 comments

Comments

@colearendt
Copy link
Contributor

colearendt commented Aug 23, 2019 •
edited
Loading

https://community.rstudio.com/t/rstudio-connect-packrat-chokes-on-bioconductor-packages/36706

This community thread discusses changes to R 3.6.0, for which:

Bioconductor packages need to be installed using BiocManager::install().

Potentially related to: #507

Particularly affects customers on RStudio Connect, who don't have a place to interactively tweak / install into the library.
@colearendt colearendt mentioned this issue Aug 23, 2019
Closed
@kevinushey
Copy link
Contributor

This should already be handled:

packrat/R/snapshot.R

Lines 341 to 357 in 29a4fdc

getBiocRepos <- function() {
BiocManager <- tryCatch(asNamespace("BiocManager"), error = identity)
if (!inherits(BiocManager, "error"))
return(BiocManager$repositories())
BiocInstaller <- tryCatch(asNamespace("BiocInstaller"), error = identity)
if (!inherits(BiocInstaller, "error"))
return(BiocInstaller$biocinstallRepos())
msg <- paste(
"Neither BiocManager nor BiocInstaller are installed;",
"cannot discover Bioconductor repositories"
)
warning(msg)
character()
}

so I'd be curious to have a reprex or similar showing the failure.

@kevinushey
Copy link
Contributor

(Perhaps the issue only occurs if both BiocInstaller and BiocManager are available and we should check BiocManager first)

@slopp
Copy link

slopp commented Sep 10, 2019

We've had another user encounter this issue, https://community.rstudio.com/t/rstudio-connect-packrat-chokes-on-bioconductor-packages/36706/7

Setting the repo option manually appeared to resolve the problem, but was anyone else able to reprex? I'd really prefer if packrat and deployments worked magically like they did before!

@MattBrauer
Copy link

title: "reprex"
author: "Matt Brauer"
date: "11/19/2019"
output: html_document

This rmd document does not deploy to the RStudio connect server, and the errors are emblematic of all attempts to publish content with Bioconductor packages.

This behavior dates to the implementation of the new BiocManager methods for package installation.

Using RStudio Version 1.2.5019 "Elderflower" (fba733f0, 2019-10-24).

The only relevant code block is this one:

knitr::opts_chunk$set(echo = TRUE)
library(Biobase)

Deploy tab output:

Preparing to deploy document...DONE
Uploading bundle for document: 2...DONE
Deploying bundle: 6 for document: 2 ...
Building R Markdown document...
Bundle requested R version 3.6.1; using /opt/R/3.6.1/bin/R which has version 3.6.1
2019/11/19 23:49:45.814444922 Using user agent string: 'RStudio R (3.6.1 x86_64-pc-linux-gnu x86_64 linux-gnu)' 
2019/11/19 23:49:46.292389124 linux distribution: Ubuntu 18.04.3 LTS (bionic) 
2019/11/19 23:49:46.293393260 # Validating R library read / write permissions --------------------------------
2019/11/19 23:49:46.293837297 R version: 3.6.1
2019/11/19 23:49:46.302856362 # Validating managed packrat installation --------------------------------------
2019/11/19 23:49:46.303299109 Vendored packrat archive: /opt/rstudio-connect/ext/R/packrat_0.5.0-15_02c203831ebac641144f4369e27dbb0d0ca021cc.tar.gz
2019/11/19 23:49:46.317271000 Vendored packrat SHA: 02c203831ebac641144f4369e27dbb0d0ca021cc
2019/11/19 23:49:46.318793902 Managed packrat SHA:  02c203831ebac641144f4369e27dbb0d0ca021cc
2019/11/19 23:49:46.319825947 Managed packrat version: 0.5.0.15
2019/11/19 23:49:46.320990355 Managed packrat is up-to-date.
2019/11/19 23:49:46.321329750 # Validating packrat cache read / write permissions ----------------------------
2019/11/19 23:49:46.381994572 Audited package hashes with local packrat installation.
2019/11/19 23:49:46.393471634 # Installing required R packages with `packrat::restore()` ---------------------
2019/11/19 23:49:46.433053909 Installing BiocGenerics (0.32.0) ... 
2019/11/19 23:49:46.666340936 curl: HTTP 200 https://cran.cnr.berkeley.edu/src/contrib/PACKAGES.rds
2019/11/19 23:49:47.474666335 curl: HTTP 404 https://cran.cnr.berkeley.edu//src/contrib/Archive/BiocGenerics/BiocGenerics_0.32.0.tar.gz
2019/11/19 23:49:47.474691465 curl: (22) The requested URL returned error: 404 Not Found
2019/11/19 23:49:48.605046496 curl: HTTP 404 https://cran.cnr.berkeley.edu//src/contrib/Archive/BiocGenerics/BiocGenerics_0.32.0.tar.gz
2019/11/19 23:49:48.605075036 curl: (22) The requested URL returned error: 404 Not Found
2019/11/19 23:49:49.730531005 curl: HTTP 404 https://cran.cnr.berkeley.edu//src/contrib/Archive/BiocGenerics/BiocGenerics_0.32.0.tar.gz
2019/11/19 23:49:49.730554845 curl: (22) The requested URL returned error: 404 Not Found
2019/11/19 23:49:50.864836914 curl: HTTP 404 https://cran.cnr.berkeley.edu//src/contrib/Archive/BiocGenerics/BiocGenerics_0.32.0.tar.gz
2019/11/19 23:49:50.864861535 curl: (22) The requested URL returned error: 404 Not Found
2019/11/19 23:49:51.993187416 curl: HTTP 404 https://cran.cnr.berkeley.edu//src/contrib/Archive/BiocGenerics/BiocGenerics_0.32.0.tar.gz
2019/11/19 23:49:51.993212307 curl: (22) The requested URL returned error: 404 Not Found
2019/11/19 23:49:52.995960452 FAILED
2019/11/19 23:49:52.996624712 Error in getSourceForPkgRecord(pkgRecord, srcDir(project), availablePackagesSource(repos = repos), : Failed to retrieve package sources for BiocGenerics 0.32.0 from CRAN (internet connectivity issue?)
2019/11/19 23:49:52.996649732 
2019/11/19 23:49:52.996684733 Unable to fully restore the R packages associated with this deployment.
2019/11/19 23:49:52.996692303 Please review the preceding messages to determine which package
2019/11/19 23:49:52.996719514 encountered installation difficulty and the cause of the failure.
2019/11/19 23:49:52.996791774 Error code: r-package-not-available

An R package required by the content cannot be found in the package repository.

Possible causes:
* The R package being installed is not available for the version of R configured at Connect.
* The R package being installed is not available for linux.
* The client computer that published the content is using a different package repository from the Connect server, and the R package being installed is not available in the repository configured at the Connect server.
* The package repository moved to a new URL after the content was published, and Connect is now attempting to rebuild the environment using the old package repository URL.

Possible solutions:
* Install a version of R on the Connect server that matches the one being used by the client computer. You can identify the required R version from the deployment logs, which will contain an entry similar to this:
  > Bundle requested R version 3.5.0; using /usr/lib/R/bin/R which has version 3.4.4
  In this example, the client computer has R 3.5.0 and the Connect server has R version 3.4.4. The recommended solution would be to install R version 3.5.0 on the Connect server alonside the existing 3.4.4 installation.
* Replace usage of Windows-specific R packages with ones available for linux.
* Configure the client with a package repository that is accessible via http(s) from the Connect server, such as CRAN or RStudio Package Manager. Reinstall the affected packages from the new repository and publish the content again.

References:
* https://docs.rstudio.com/connect/admin/getting-started.html#installation
* https://support.rstudio.com/hc/en-us/articles/360004067074-Managing-Packages-with-RStudio

2019/11/19 23:49:52.996791774 Additional data:
Package: 'BiocGenerics'
PackageVersion: '0.32.0'
Repository: 'CRAN'
Found in the following log entry:
2019/11/19 23:49:52.996624712 Error in getSourceForPkgRecord(pkgRecord, srcDir(project), availablePackagesSource(repos = repos), : Failed to retrieve package sources for BiocGenerics 0.32.0 from CRAN (internet connectivity issue?)
Build error: r-package-not-available
Document deployment failed with error: r-package-not-available
Deployment completed: http://ec2-52-41-171-115.us-west-2.compute.amazonaws.com:443/connect/#/apps/2/logs

sessionInfo()

## R version 3.6.1 (2019-07-05)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS Mojave 10.14.5
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] parallel  stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
## [1] Biobase_2.46.0      BiocGenerics_0.32.0
## 
## loaded via a namespace (and not attached):
##  [1] compiler_3.6.1  magrittr_1.5    tools_3.6.1     htmltools_0.4.0
##  [5] yaml_2.2.0      Rcpp_1.0.2      stringi_1.4.3   rmarkdown_1.16 
##  [9] knitr_1.25      stringr_1.4.0   xfun_0.10       digest_0.6.21  
## [13] rlang_0.4.1     evaluate_0.14

packrat::.snapshotImpl(project=".", snapshot.sources = FALSE)

packrat/packrat.lock:

PackratFormat: 1.4
PackratVersion: 0.5.0
RVersion: 3.6.1
Repos: CRAN=https://cran.cnr.berkeley.edu/

Package: BH
Source: CRAN
Version: 1.69.0-1
Hash: 15f597ed227897f4f793b6161260f4b9

Package: Biobase
Source: Bioconductor
Version: 2.46.0
Hash: 8cafc212f9d20d470843c13c4988771c
Requires: BiocGenerics

Package: BiocGenerics
Source: Bioconductor
Version: 0.32.0
Hash: b64f82cc8788075b3d2b3c85d879fbf4

Package: BiocManager
Source: CRAN
Version: 1.30.9
Hash: 0dc0169c4d82275fdf64cdd8dfb27311

Package: BiocParallel
Source: Bioconductor
Version: 1.20.0
Hash: 7c2fbb5b10c0cbfcedafc1a23252a18e
Requires: BH, snow, futile.logger

Package: BiocSingular
Source: Bioconductor
Version: 1.2.0
Hash: 9794dec94cf8de081f2b92f109a92f67
Requires: BiocGenerics, Rcpp, S4Vectors, Matrix, irlba, rsvd,
    BiocParallel, DelayedArray, beachmat

Package: Biostrings
Source: Bioconductor
Version: 2.54.0
Hash: 6ee01dc158e4e9ac2deb76e3601b7628
Requires: BiocGenerics, S4Vectors, IRanges, XVector

Package: DBI
Source: CRAN
Version: 1.0.0
Hash: 6abedd7919c4457604c0aa44529a6683

Package: DT
Source: CRAN
Version: 0.9
Hash: f72fd6ee6cf1656384503d6c7ca6cd96
Requires: jsonlite, magrittr, htmltools, htmlwidgets, promises,
    crosstalk

Package: DelayedArray
Source: Bioconductor
Version: 0.12.0
Hash: 46d534f790b01cd3f87909f43ef69922
Requires: BiocGenerics, matrixStats, S4Vectors, Matrix, IRanges,
    BiocParallel

Package: IRanges
Source: Bioconductor
Version: 2.20.0
Hash: 9f4cd7582c0ec4742fe2ac6e02fd5d52
Requires: BiocGenerics, S4Vectors

Package: KernSmooth
Source: CRAN
Version: 2.23-16
Hash: 15a3c9bf1c258139c15c8fbe7cff24cf

Package: MASS
Source: CRAN
Version: 7.3-51.4
Hash: 35b5e96d2946a20836d838f537bc7ab9

Package: Matrix
Source: CRAN
Version: 1.2-17
Hash: 3ee56b7c430e66a6222cf6d700788888
Requires: lattice

Package: R6
Source: CRAN
Version: 2.4.0
Hash: 948a547c484e5bea15eee76cc53cce3f

Package: RColorBrewer
Source: CRAN
Version: 1.1-2
Hash: c0d56cd15034f395874c870141870c25

Package: RCurl
Source: CRAN
Version: 1.95-4.12
Hash: 261163f9c66d2a2c7ef8028765ed2838
Requires: bitops

Package: Rcpp
Source: CRAN
Version: 1.0.2
Hash: d04e441a8d398e3d3a71f294c07fa94d

Package: RcppThread
Source: CRAN
Version: 0.5.4
Hash: e447c8362fe9921c64fedf40a67b56c6

Package: Rdpack
Source: CRAN
Version: 0.11-0
Hash: 4a9b3dce48656f59e3da322f20442099
Requires: gbRd, bibtex

Package: S4Vectors
Source: Bioconductor
Version: 0.24.0
Hash: aad4c19e1d3f65832e0d82ee0b30f068
Requires: BiocGenerics

Package: XVector
Source: Bioconductor
Version: 0.26.0
Hash: 282c9ea56852a3973d23772e892f16df
Requires: BiocGenerics, zlibbioc, S4Vectors, IRanges

Package: antiword
Source: CRAN
Version: 1.3
Hash: d52799bc9a62d2e67660d4dfbcda463e
Requires: sys

Package: ape
Source: CRAN
Version: 5.3
Hash: b8f490bfc28c372922ec04ea961fbe30
Requires: Rcpp, lattice, nlme

Package: askpass
Source: CRAN
Version: 1.1
Hash: 6f6c430e3cd0dd7d48f447700f4d7e7f
Requires: sys

Package: assertthat
Source: CRAN
Version: 0.2.1
Hash: 622be49032fe50bd42e96aaef613e209

Package: backports
Source: CRAN
Version: 1.1.5
Hash: 35ad64fcf2063e2a52031b0f1a59d8f0

Package: base64enc
Source: CRAN
Version: 0.1-3
Hash: c590d29e555926af053055e23ee79efb

Package: beachmat
Source: Bioconductor
Version: 2.2.0
Hash: 00cef708061d3f96a7b2720101dd5a5d
Requires: BiocGenerics, Matrix, DelayedArray

Package: bibtex
Source: CRAN
Version: 0.4.2
Hash: 58c21a98bdd9c67ec0b01d589988681a
Requires: stringr

Package: bitops
Source: CRAN
Version: 1.0-6
Hash: 67d0775189fd0041d95abca618c5c07e

Package: broom
Source: CRAN
Version: 0.5.2
Hash: 2c1abd749c826a39101a156ed0afc9be
Requires: backports, generics, nlme, purrr, stringr, reshape2, tibble,
    dplyr, tidyr

Package: caTools
Source: CRAN
Version: 1.17.1.2
Hash: 4e16b54f85b1a69e05021a81fda1aef1
Requires: bitops

Package: callr
Source: CRAN
Version: 3.3.2
Hash: 7661e5194cbbe511957b2fb621516c1b
Requires: R6, processx

Package: cellranger
Source: CRAN
Version: 1.1.0
Hash: be9d203e7849f73818b36f93e9273c2c
Requires: rematch, tibble

Package: cli
Source: CRAN
Version: 1.1.0
Hash: bc4e54014c2049f2605ad0c3ba0cce6b
Requires: assertthat, crayon

Package: clipr
Source: CRAN
Version: 0.7.0
Hash: 30cdec6c8cc62c80c485e6bdd0c02b05

Package: colorspace
Source: CRAN
Version: 1.4-1
Hash: 60a56e9998b8b58ee378db3dc91b27a5

Package: crayon
Source: CRAN
Version: 1.3.4
Hash: ff2840dd9b0d563fc80377a5a45510cd

Package: crosstalk
Source: CRAN
Version: 1.0.0
Hash: c13adea5906fbe2becfcb5f843b26749
Requires: R6, jsonlite, lazyeval, htmltools, shiny, ggplot2

Package: curl
Source: CRAN
Version: 4.2
Hash: 3d7392b36f838a538683f98e580f35dd

Package: data.table
Source: CRAN
Version: 1.12.6
Hash: 4fbfebe60de9b5c065ba21f37c68e544

Package: dbplyr
Source: CRAN
Version: 1.4.2
Hash: 98ff6c6b2ff30fd4007dd16c75027b30
Requires: DBI, R6, assertthat, glue, rlang, purrr, tidyselect, tibble,
    dplyr

Package: digest
Source: CRAN
Version: 0.6.21
Hash: b75f091dd438a0ed4d858a3e415e054c

Package: dplyr
Source: CRAN
Version: 0.8.3
Hash: 201287c2b23cff8b2ef156ec8b1e57f2
Requires: BH, R6, Rcpp, assertthat, glue, magrittr, pkgconfig, plogr,
    rlang, tidyselect, tibble

Package: dtplyr
Source: CRAN
Version: 0.0.3
Hash: 2607d82572267dd8b4246ed3ce232722
Requires: data.table, lazyeval, rlang, dplyr

Package: ellipsis
Source: CRAN
Version: 0.3.0
Hash: 30b58109e4d7c6184a9c2e32f9ae38c6
Requires: rlang

Package: evaluate
Source: CRAN
Version: 0.14
Hash: 18306cc3bc1aec7b7360eea8a0eb0ee1

Package: fansi
Source: CRAN
Version: 0.4.0
Hash: f147621f72b561485bfffcae78c4f5d5

Package: fastmap
Source: CRAN
Version: 1.0.1
Hash: d272cd728e4095b3964181b44763f46c

Package: forcats
Source: CRAN
Version: 0.4.0
Hash: 3999d0f4538fe92c7af47b82f3e461b8
Requires: magrittr, rlang, ellipsis, tibble

Package: formatR
Source: CRAN
Version: 1.7
Hash: 60dec134ecd2fd23c658b8057c76317a

Package: fs
Source: CRAN
Version: 1.3.1
Hash: 104f1ba37405da6eb4d2391f7c02aaba
Requires: Rcpp

Package: futile.logger
Source: CRAN
Version: 1.4.3
Hash: d1cc6584b39f2c4cfbe377fd94cbdbaa
Requires: futile.options, lambda.r

Package: futile.options
Source: CRAN
Version: 1.0.1
Hash: c5a7e0ce07509a8561881c8860270d71

Package: gbRd
Source: CRAN
Version: 0.4-11
Hash: 076595e100cc96156ef0a15a2d6fa00d

Package: gdata
Source: CRAN
Version: 2.18.0
Hash: f4fdf56bd81ae3e1d42379678b472a34
Requires: gtools

Package: generics
Source: CRAN
Version: 0.0.2
Hash: 4aaf002dd434e8c854611c5d11a1d58e

Package: ggplot2
Source: CRAN
Version: 3.2.1
Hash: 7cf3f9df0089475f133ec23befca1032
Requires: MASS, digest, gtable, lazyeval, rlang, viridisLite, withr,
    scales, mgcv, reshape2, tibble

Package: ggseqlogo
Source: CRAN
Version: 0.1
Hash: 707ab321ac308f027578271f710ea674
Requires: ggplot2

Package: ggtree
Source: Bioconductor
Version: 2.0.0
Hash: a66ac05469d774ef60f08c0a2b36adaa
Requires: magrittr, rlang, purrr, rvcheck, ape, dplyr, ggplot2, tidyr,
    tidytree, treeio

Package: ggupset
Source: CRAN
Version: 0.1.0
Hash: 99ad60e62012cb2809e14902b141e0b1
Requires: gtable, rlang, scales, tibble, ggplot2

Package: glue
Source: CRAN
Version: 1.3.1
Hash: 660bbbe3803c7cf7c9489a7d99a9c0ed

Package: gplots
Source: CRAN
Version: 3.0.1.1
Hash: ee14c65104be85d41d3efb15efa78eed
Requires: KernSmooth, gtools, caTools, gdata

Package: gtable
Source: CRAN
Version: 0.3.0
Hash: a9e7b0666eb933a0cb36779240b4462e

Package: gtools
Source: CRAN
Version: 3.8.1
Hash: 6cb09dd6faf3aeac5c5acae55bfa6495

Package: haven
Source: CRAN
Version: 2.1.1
Hash: 68fe47f9b101144fd042b7514a16313e
Requires: Rcpp, hms, tibble, forcats, readr

Package: highr
Source: CRAN
Version: 0.8
Hash: 16aa2cc98d7b68c9d148c263c8dcdbcd

Package: hms
Source: CRAN
Version: 0.5.2
Hash: 47b5ab7b81a91620766782f912924611
Requires: pkgconfig, rlang, vctrs

Package: htmltools
Source: CRAN
Version: 0.4.0
Hash: 3f49193aa22146296cee8ae091b6303a
Requires: Rcpp, digest, rlang

Package: htmlwidgets
Source: CRAN
Version: 1.5.1
Hash: 20e5cc02b795afc7322836c947b5aab2
Requires: jsonlite, yaml, htmltools

Package: httpuv
Source: CRAN
Version: 1.5.2
Hash: bedc97351732877695aa0f20e32d6ad9
Requires: BH, R6, Rcpp, later, promises

Package: httr
Source: CRAN
Version: 1.4.1
Hash: cc16de93eaabd3c6d0785cb8e6d059ab
Requires: R6, curl, jsonlite, mime, openssl

Package: irlba
Source: CRAN
Version: 2.3.3
Hash: b54c77f8a47a3d33dd738d5ae9d491bf
Requires: Matrix

Package: jsonlite
Source: CRAN
Version: 1.6
Hash: 5f969e213e966135393e3e304abf3f49

Package: knitr
Source: CRAN
Version: 1.25
Hash: c0b5316240a79d38f4785884b95a9609
Requires: evaluate, highr, xfun, yaml, stringr, markdown

Package: labeling
Source: CRAN
Version: 0.3
Hash: ecf589b42cd284b03a4beb9665482d3e

Package: lambda.r
Source: CRAN
Version: 1.2.4
Hash: ee5a211007a3e55caafe1b90ab4b5093
Requires: formatR

Package: later
Source: CRAN
Version: 1.0.0
Hash: 205ee1ecb9ea284441563fc014b45ece
Requires: BH, Rcpp, rlang

Package: lattice
Source: CRAN
Version: 0.20-38
Hash: 45211081d39bb6d5a89fd789105901aa

Package: lazyeval
Source: CRAN
Version: 0.2.2
Hash: 563563691bea3cde6945a98996d7c166

Package: lifecycle
Source: CRAN
Version: 0.1.0
Hash: fd2ceffa778c010fab2df12b2eccd835
Requires: glue, rlang

Package: lubridate
Source: CRAN
Version: 1.7.4
Hash: 1ea7526e3b50f96340b9a4a1c7521809
Requires: Rcpp, stringr

Package: magrittr
Source: CRAN
Version: 1.5
Hash: bdc4d48c3135e8f3b399536ddf160df4

Package: markdown
Source: CRAN
Version: 1.1
Hash: 1b6a18fd395589425e338a47b999099f
Requires: mime, xfun

Package: matrixStats
Source: CRAN
Version: 0.55.0
Hash: 8d3c061bc15125a730ea292449c5e0aa

Package: mgcv
Source: CRAN
Version: 1.8-28
Hash: 065e3500f08942b22db2ff1fab0008cd
Requires: Matrix, nlme

Package: mime
Source: CRAN
Version: 0.7
Hash: 0d7563caf453c231b6f8c359c51eecc2

Package: modelr
Source: CRAN
Version: 0.1.5
Hash: c79fcf8da71e70be2d19cd9c505225ca
Requires: magrittr, rlang, purrr, tibble, dplyr, tidyr, broom

Package: munsell
Source: CRAN
Version: 0.5.0
Hash: 38d0efee9bb99bef143bde41c4ce715c
Requires: colorspace

Package: ndjson
Source: CRAN
Version: 0.7.0
Hash: 70a20b6426ea0637701e9887fb3a4d12
Requires: Rcpp, data.table, dplyr, dtplyr

Package: nlme
Source: CRAN
Version: 3.1-141
Hash: 011c066e63a30a0a0462dfe1503cb506
Requires: lattice

Package: openssl
Source: CRAN
Version: 1.4.1
Hash: b01fe6ae05ec2a30a777dc338af5bf69
Requires: askpass

Package: packrat
Source: CRAN
Version: 0.5.0
Hash: 498643e765d1442ba7b1160a1df3abf9

Package: pdftools
Source: CRAN
Version: 2.2
Hash: f59676f510f9bb02d2d648a5cdf237e7
Requires: Rcpp, qpdf

Package: pillar
Source: CRAN
Version: 1.4.2
Hash: 28ff1862b4e0c8761efca442e80a63d8
Requires: crayon, fansi, rlang, utf8, cli, vctrs

Package: piton
Source: CRAN
Version: 0.1.1
Hash: 8dd182e268c72b8891b2ab55f1768eb8
Requires: Rcpp

Package: pkgconfig
Source: CRAN
Version: 2.0.3
Hash: 5ff5f2361851a49534c96caa2a8071c7

Package: plogr
Source: CRAN
Version: 0.2.0
Hash: 81a8008a5e7858552503935f1abe48aa

Package: plyr
Source: CRAN
Version: 1.8.4
Hash: 5c3737d7c1846e30d40c8c38110b5fcd
Requires: Rcpp

Package: prettyunits
Source: CRAN
Version: 1.0.2
Hash: 49286102a855640daaa38eafe8b1ec30
Requires: assertthat, magrittr

Package: processx
Source: CRAN
Version: 3.4.1
Hash: 5c1f432b290b26ccc2aaaa8ff1fd2f62
Requires: R6, ps

Package: progress
Source: CRAN
Version: 1.2.2
Hash: 209280eb751acf5899f7c69366e14bd3
Requires: R6, crayon, prettyunits, hms

Package: promises
Source: CRAN
Version: 1.1.0
Hash: 0404586e7e8dff0de5fde4a65f37e39b
Requires: R6, Rcpp, magrittr, rlang, later

Package: ps
Source: CRAN
Version: 1.3.0
Hash: 1d4cae95887ffe5b1a22bea5994476cd

Package: purrr
Source: CRAN
Version: 0.3.3
Hash: d4f497f8a97ef6c7182a87b2476748d1
Requires: magrittr, rlang

Package: qpdf
Source: CRAN
Version: 1.1
Hash: ca4eaa18c29186f6fec363c3e973dd5b
Requires: Rcpp, curl, askpass

Package: readODS
Source: CRAN
Version: 1.6.7
Hash: a0451cbb006f3d4b3d07f55db301b74e
Requires: stringi, xml2, cellranger, readr

Package: readr
Source: CRAN
Version: 1.3.1
Hash: c45e5ec73f9bf1d1bdc1e4c6e6a87011
Requires: BH, R6, Rcpp, clipr, crayon, hms, tibble

Package: readtext
Source: CRAN
Version: 0.75
Hash: 66e8a9ab5e6470273c8bb1300fad40a0
Requires: data.table, digest, jsonlite, stringi, xml2, antiword,
    striprtf, httr, pdftools, tibble, readxl, readODS, streamR

Package: readxl
Source: CRAN
Version: 1.3.1
Hash: 5d7697abddc48ab778f9b41486ec0b61
Requires: Rcpp, progress, tibble, cellranger

Package: rematch
Source: CRAN
Version: 1.0.1
Hash: ad4faf59e7611117ff165817074c50c7

Package: reprex
Source: CRAN
Version: 0.3.0
Hash: 2029355cb70894267c2c7557c79307fd
Requires: clipr, rlang, whisker, withr, fs, callr, rmarkdown

Package: reshape2
Source: CRAN
Version: 1.4.3
Hash: b7ea8a2e7a9df39c2346e78bd83e26f8
Requires: Rcpp, plyr, stringr

Package: rjson
Source: CRAN
Version: 0.2.20
Hash: 44ee331003bf03b92e97b3089461dd2f

Package: rlang
Source: CRAN
Version: 0.4.1
Hash: 686b7c4593f009713b9df03a2bb33124

Package: rmarkdown
Source: CRAN
Version: 1.16
Hash: 1f3014c40b12e8af0abf39fd78080237
Requires: base64enc, evaluate, jsonlite, mime, xfun, yaml, htmltools,
    stringr, tinytex, knitr

Package: rstudioapi
Source: CRAN
Version: 0.10
Hash: 63f43c6ff14d92e1d65ca6c21d45a1eb

Package: rsvd
Source: CRAN
Version: 1.0.2
Hash: 52c977ed3c5438c7030c5c5d3994c4dc
Requires: Matrix

Package: rvcheck
Source: CRAN
Version: 0.1.6
Hash: fb2a0a166a0e8a51826ecca57a942544
Requires: BiocManager, rlang

Package: rvest
Source: CRAN
Version: 0.3.4
Hash: f183d7dabd2bf9d967bfa53a777955f4
Requires: magrittr, xml2, selectr, httr

Package: scales
Source: CRAN
Version: 1.0.0
Hash: f4f1b13b6774ee3122a36466d1bc50b8
Requires: R6, RColorBrewer, Rcpp, labeling, viridisLite, munsell

Package: selectr
Source: CRAN
Version: 0.4-1
Hash: b12802c11e35dec9d16a74d30ed0f3ed
Requires: R6, stringr

Package: shiny
Source: CRAN
Version: 1.4.0
Hash: 7a1d8725849ecb792b4df2c084769c23
Requires: R6, crayon, digest, fastmap, jsonlite, mime, rlang,
    sourcetools, xtable, htmltools, later, promises, httpuv

Package: shinyBS
Source: CRAN
Version: 0.61
Hash: 4644935bd93e62a0b82686b26af7efc2
Requires: htmltools, shiny

Package: shinyDND
Source: CRAN
Version: 0.1.0
Hash: 54f7d8f4f332c1bb4d1681ce77246c4b
Requires: htmltools, shiny

Package: snow
Source: CRAN
Version: 0.4-3
Hash: 350fc9078c96345a2246415fc9e67311

Package: sourcetools
Source: CRAN
Version: 0.1.7
Hash: d093478ac90064e670cd4bf1a99b47b6

Package: streamR
Source: CRAN
Version: 0.4.5
Hash: fd893c8cb7c565611f3ae0fc97e6655b
Requires: rjson, RCurl, ndjson

Package: stringi
Source: CRAN
Version: 1.4.3
Hash: ed2a82fc7cc668c1345223d938cdfaf2

Package: stringr
Source: CRAN
Version: 1.4.0
Hash: 67da32dbb2a7a16f2ef124336358e54a
Requires: glue, magrittr, stringi

Package: striprtf
Source: CRAN
Version: 0.5.2
Hash: 180d4f1c312237739368e646624a0775
Requires: Rcpp, magrittr, stringr

Package: sys
Source: CRAN
Version: 3.3
Hash: d5a4afad9298f42aae77f6389713a066

Package: tibble
Source: CRAN
Version: 2.1.3
Hash: f59680d81ddc45fa3fcb8c07686d1d89
Requires: crayon, fansi, pkgconfig, rlang, cli, pillar

Package: tidyr
Source: CRAN
Version: 1.0.0
Hash: 52f95ddff9a8bbc8e5d7dc0050d6cda4
Requires: Rcpp, glue, magrittr, rlang, stringi, ellipsis, lifecycle,
    purrr, vctrs, tidyselect, tibble, dplyr

Package: tidyselect
Source: CRAN
Version: 0.2.5
Hash: 9ab4ed03f4b7bbdbd1db9d7a920aae1a
Requires: Rcpp, glue, rlang, purrr

Package: tidytree
Source: CRAN
Version: 0.2.9
Hash: 125014578488ae97eedcce80ff056c6e
Requires: lazyeval, magrittr, rlang, ape, tibble, dplyr

Package: tidyverse
Source: CRAN
Version: 1.2.1
Hash: 1b090209cb20b6fc6eba75de8b7f0b53
Requires: crayon, jsonlite, magrittr, rlang, rstudioapi, xml2, cli,
    purrr, stringr, lubridate, hms, httr, tibble, rvest, reprex, dplyr,
    forcats, ggplot2, readr, readxl, dbplyr, tidyr, haven, broom,
    modelr

Package: tidyxl
Source: CRAN
Version: 1.0.4
Hash: 2e76f74c7bc837afddf2923220426622
Requires: Rcpp, piton

Package: tinytex
Source: CRAN
Version: 0.17
Hash: 9da7bd371440e0f6b3bbe26cda55e374
Requires: xfun

Package: treeio
Source: Bioconductor
Version: 1.10.0
Hash: 0b1afd4c2f7fbfefc91ff527f727523e
Requires: jsonlite, magrittr, rlang, ape, tibble, dplyr, tidytree

Package: universalmotif
Source: Bioconductor
Version: 1.4.0
Hash: df006d70136a15f477d212741c827325
Requires: BiocGenerics, MASS, Rcpp, RcppThread, rlang, yaml, S4Vectors,
    processx, ape, Rdpack, Biostrings, ggplot2, ggseqlogo, ggtree

Package: utf8
Source: CRAN
Version: 1.1.4
Hash: f3f97ce59092abc8ed3fd098a59e236c

Package: vctrs
Source: CRAN
Version: 0.2.0
Hash: daf77cb3dbcacd7fb619cb3748dc215f
Requires: backports, digest, glue, rlang, zeallot, ellipsis

Package: viridisLite
Source: CRAN
Version: 0.3.0
Hash: 78bb072c4f9e729a283d4c40ec93f9c6

Package: whisker
Source: CRAN
Version: 0.4
Hash: 5b1ec05cd96c1e0c6048bab49abee3aa

Package: withr
Source: CRAN
Version: 2.1.2
Hash: d534108bcd5f34ec73e9eb523751ba20

Package: xfun
Source: CRAN
Version: 0.10
Hash: 83f0de50249d263dfbce9b3aa6d3109a

Package: xml2
Source: CRAN
Version: 1.2.2
Hash: c5258a3beb15da46d4682eda667bf5ec
Requires: Rcpp

Package: xtable
Source: CRAN
Version: 1.8-4
Hash: dc0d47261b678d26032363bebd050540

Package: yaml
Source: CRAN
Version: 2.2.0
Hash: a5ad5616d83d89f8d84cbf3cf4034e13

Package: zeallot
Source: CRAN
Version: 0.1.0
Hash: 10b2ed48e202b4db421ae864041dc4b2

Package: zlibbioc
Source: Bioconductor
Version: 1.32.0
Hash: 5fadfb71ee7cd5fe6b00762e79b56cf8

@kevinushey
Copy link
Contributor

Repos: CRAN=https://cran.cnr.berkeley.edu/

The simplest way to fix this is to ensure the Bioconductor repositories get set in the lockfile; e.g. something like:

options(repos = BiocManager::repositories())
# deploy application with Bioc repos active

@slopp
Copy link

slopp commented Jan 3, 2020

@kevinushey we had another customer hit this issue today - do you know why the repos would not be active? It definitely appears that setting repos solves the problem, but it isn't clear to me why the code in packrat to recognize the repos isn't triggering.

It would be awesome if we could poke at this some more, as it is becoming a recurring problem for support.

@kevinushey
Copy link
Contributor

I'm OOF so won't be able to take a look until next week.

@rstub
Copy link
Member

rstub commented Jan 6, 2020

Summarizing what @slopp found concerning this most recent issue:

@kevinushey
Copy link
Contributor

Packrat should already be handling this properly:

packrat/R/pkg.R

Lines 299 to 316 in 448aafd

if (length(df$GithubRepo) || hasRemoteType(df, "github")) {
# It's GitHub!
return(structure(c(list(
name = name,
source = 'github',
version = ver,
gh_repo = as.character(df$GithubRepo),
gh_username = as.character(df$GithubUsername),
gh_ref = as.character(df$GithubRef),
gh_sha1 = as.character(df$GithubSHA1)),
c(gh_subdir = as.character(df$GithubSubdir)),
c(remote_host = as.character(df$RemoteHost)),
c(remote_repo = as.character(df$RemoteRepo)),
c(remote_username = as.character(df$RemoteUsername)),
c(remote_ref = as.character(df$RemoteRef)),
c(remote_sha = as.character(df$RemoteSha))
), class = c('packageRecord', 'github')))
} else if (hasRemoteType(df, "bitbucket")) {

Packrat checks whether the package is from GitHub before querying the biocViews field, and BiocManager::install() appears to add those fields to the installed package's DESCRIPTION file.

@slopp
Copy link

slopp commented Jan 6, 2020

@kevinushey I was able to re-produce an error by:

  1. Uisng BiocManager to install:
BiocManager::install('romanhaa/cerebroApp')
  1. Writing a basic skeleton app that had:
library(shiny)
library(cerebroApp)
ui <- fluidPage()
server <- function(input, output){}
shinyApp(ui=ui, server=server)
  1. Attempting to deploy to RStudio Connect, after setting the repo option to BiocManager::repositories()

The deployment log showed that packrat was looking for the cerberoApp package within the BioCsoft repository archive.

@kevinushey
Copy link
Contributor

After a snapshot, I see in the lockfile:

Package: cerebroApp
Source: github
Version: 1.1.1
Hash: 4b9b358afc809ddf3e820f01c53d8a0c
Requires: DT, GSVA, Matrix, biomaRt, dplyr, formattable, future.apply,
    ggplot2, ggtree, httr, igraph, msigdbr, pbapply, plotly, qvalue,
    readr, reshape2, shiny, shinyWidgets, shinydashboard, tibble, tidyr
GithubRepo: cerebroApp
GithubUsername: romanhaa
GithubRef: master
GithubSha1: b89b964200f5c2f7ac68f413479bfe06df7b3881
RemoteHost: api.github.com
RemoteRepo: cerebroApp
RemoteUsername: romanhaa
RemoteRef: master
RemoteSha: b89b964200f5c2f7ac68f413479bfe06df7b3881

I also see the package source correctly annotated when reading the lockfile:

> packrat:::readLockFilePackages("packrat/packrat.lock")$cerebroApp
$name
[1] "cerebroApp"

$source
[1] "github"

$version
[1] "1.1.1"

$requires
 [1] "DT"             "GSVA"           "Matrix"         "biomaRt"
 [5] "dplyr"          "formattable"    "future.apply"   "ggplot2"
 [9] "ggtree"         "httr"           "igraph"         "msigdbr"
[13] "pbapply"        "plotly"         "qvalue"         "readr"
[17] "reshape2"       "shiny"          "shinyWidgets"   "shinydashboard"
[21] "tibble"         "tidyr"

$hash
[1] "4b9b358afc809ddf3e820f01c53d8a0c"

Note that you need the development version of Packrat if your copy of remotes isn't writing out the Github* fields.

@gmrukwa
Copy link

gmrukwa commented Oct 2, 2021

If anyone else is on this issue due to problems with restoring the environment from both CRAN and Bioconductor, on my end the problem was packrat not saving the repos as metadata to the lock file when making a snapshot. Fortunately, I had the old env, so I've replaced:

Repos: CRAN=https://cran.rstudio.com

with

Repos: CRAN=https://cran.microsoft.com/snapshot/2021-07-10,
    BioCsoft=https://bioconductor.org/packages/3.10/bioc,
    BioCann=https://bioconductor.org/packages/3.10/data/annotation,
    BioCexp=https://bioconductor.org/packages/3.10/data/experiment,
    BioCworkflows=https://bioconductor.org/packages/3.10/workflows

Of course the exact values will depend on your specific environment, but the above resolved major part of the issue. You can use packrat::set_lockfile_metadata(repos=r) for that, provided that you saved the above repos config in variable r.

Another problem was related to package BiocGenerics installation which apparently doesn't require BiocManager to be installed. I've added it manually as extra requirement and now it works.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
6 participants
@MattBrauer @gmrukwa @kevinushey @slopp @colearendt @rstub