remotes in ubuntu-rchk builder
romainfrancois opened this issue · 5 comments
romainfrancois commented
I had a PREPERROR (see below) when trying to rhub::check(platform = "ubuntu-rchk") with the Rcpp remote set to
Remotes:
romainfrancois/Rcpp@rchk-VOID_END_RCPP
So that I could try a less noisy Rcpp/rchk combo, i.e. RcppCore/Rcpp#949
romainfrancois commented
full PREPERROR results from https://builder.r-hub.io/status/original/dplyr_0.8.0.9008.tar.gz-156bd5d47d49482b849cecda2496c4a1
Started by user r-hub Jenkins admin
Building remotely on 10.2.0.5-86c1b2e7 (slave swarm linux) in workspace /home/ubuntu/workspace/dplyr_0.8.0.9008.tar.gz-156bd5d47d49482b849cecda2496c4a1
[dplyr_0.8.0.9008.tar.gz-156bd5d47d49482b849cecda2496c4a1] $ /bin/sh -xe /tmp/hudson6897930133839176418.sh
+R-HUB-R-HUB-R-HUBdate -u +%Y-%m-%dT%H:%M:%SZ
+R-HUB-R-HUB-R-HUBwget https://builder.r-hub.io/build/in-progress/dplyr_0.8.0.9008.tar.gz-156bd5d47d49482b849cecda2496c4a1/2019-03-14T06:13:44Z
--2019-03-14 06:13:44-- https://builder.r-hub.io/build/in-progress/dplyr_0.8.0.9008.tar.gz-156bd5d47d49482b849cecda2496c4a1/2019-03-14T06:13:44Z
Resolving builder.r-hub.io (builder.r-hub.io)... 54.241.228.251
Connecting to builder.r-hub.io (builder.r-hub.io)|54.241.228.251|:443... connected.
HTTP request sent, awaiting response... 200 OK
Syntax error in Set-Cookie: r-hub frontend=s%3Adb8ac21a-cc0a-4c13-af69-d2eb6481d593.Qhgs%2FbvT3MJbjDJeBYtw7Cz2CdBDgdLWd7N7M7nqhMA; Path=/; Expires=Thu, 14 Mar 2019 16:13:44 GMT at position 0.
Length: unspecified [application/json]
Saving to: '2019-03-14T06:13:44Z'
0K 1.59M=0s
2019-03-14 06:13:44 (1.59 MB/s) - '2019-03-14T06:13:44Z' saved [15]
+R-HUB-R-HUB-R-HUBdocker run --user docker --rm rhub/ubuntu-rchk bash -c echo $RHUB_PLATFORM
+R-HUB-R-HUB-R-HUBexport RHUB_PLATFORM=linux-x86_64-ubuntu-gcc
+R-HUB-R-HUB-R-HUBecho >>>>>==================== Downloading and unpacking package file
>>>>>==================== Downloading and unpacking package file
+R-HUB-R-HUB-R-HUBwget -O dplyr_0.8.0.9008.tar.gz https://builder.r-hub.io/file/0c868f5e9fb048128e648bcd92f0b29e
--2019-03-14 06:13:45-- https://builder.r-hub.io/file/0c868f5e9fb048128e648bcd92f0b29e
Resolving builder.r-hub.io (builder.r-hub.io)... 54.241.228.251
Connecting to builder.r-hub.io (builder.r-hub.io)|54.241.228.251|:443... connected.
HTTP request sent, awaiting response... 200 OK
Syntax error in Set-Cookie: r-hub frontend=s%3A0e51985a-e353-43f1-831b-7e84ae25d79a.LqOQgsI0PwCN3OjdugkvqMijZ6N1nJw%2Bl482mPPlrGc; Path=/; Expires=Thu, 14 Mar 2019 16:13:45 GMT at position 0.
Length: 1143302 (1.1M) [application/octet-stream]
Saving to: 'dplyr_0.8.0.9008.tar.gz'
0K .......... .......... .......... .......... .......... 4% 8.40M 0s
50K .......... .......... .......... .......... .......... 8% 9.21M 0s
100K .......... .......... .......... .......... .......... 13% 9.99M 0s
150K .......... .......... .......... .......... .......... 17% 11.7M 0s
200K .......... .......... .......... .......... .......... 22% 13.5M 0s
250K .......... .......... .......... .......... .......... 26% 10.6M 0s
300K .......... .......... .......... .......... .......... 31% 20.8M 0s
350K .......... .......... .......... .......... .......... 35% 11.8M 0s
400K .......... .......... .......... .......... .......... 40% 19.4M 0s
450K .......... .......... .......... .......... .......... 44% 9.93M 0s
500K .......... .......... .......... .......... .......... 49% 18.9M 0s
550K .......... .......... .......... .......... .......... 53% 15.7M 0s
600K .......... .......... .......... .......... .......... 58% 14.0M 0s
650K .......... .......... .......... .......... .......... 62% 14.7M 0s
700K .......... .......... .......... .......... .......... 67% 24.0M 0s
750K .......... .......... .......... .......... .......... 71% 21.4M 0s
800K .......... .......... .......... .......... .......... 76% 21.3M 0s
850K .......... .......... .......... .......... .......... 80% 18.4M 0s
900K .......... .......... .......... .......... .......... 85% 19.3M 0s
950K .......... .......... .......... .......... .......... 89% 31.3M 0s
1000K .......... .......... .......... .......... .......... 94% 22.8M 0s
1050K .......... .......... .......... .......... .......... 98% 87.6M 0s
1100K .......... ...... 100% 8.92M=0.07s
2019-03-14 06:13:45 (15.0 MB/s) - 'dplyr_0.8.0.9008.tar.gz' saved [1143302/1143302]
+R-HUB-R-HUB-R-HUB+R-HUB-R-HUB-R-HUBgrep ^[^/]*/DESCRIPTION$
tar tzf dplyr_0.8.0.9008.tar.gz
+R-HUB-R-HUB-R-HUBDESC=dplyr/DESCRIPTION
+R-HUB-R-HUB-R-HUBtar xzf dplyr_0.8.0.9008.tar.gz dplyr/DESCRIPTION
+R-HUB-R-HUB-R-HUBecho >>>>>==================== Querying system requirements
>>>>>==================== Querying system requirements
+R-HUB-R-HUB-R-HUBRscript -e library(sysreqs); cat(sysreq_commands("dplyr/DESCRIPTION"))
+R-HUB-R-HUB-R-HUBsysreqs=export DEBIAN_FRONTEND=noninteractive; apt-get -y update && apt-get install -y git-core pandoc pandoc-citeproc libmariadb-client-lgpl-dev libpq-dev make libssl-dev libcurl4-openssl-dev
+R-HUB-R-HUB-R-HUBrm dplyr/DESCRIPTION
+R-HUB-R-HUB-R-HUBecho >>>>>==================== Installing system requirements
>>>>>==================== Installing system requirements
+R-HUB-R-HUB-R-HUB[ ! -z export DEBIAN_FRONTEND=noninteractive; apt-get -y update && apt-get install -y git-core pandoc pandoc-citeproc libmariadb-client-lgpl-dev libpq-dev make libssl-dev libcurl4-openssl-dev ]
+R-HUB-R-HUB-R-HUBecho export DEBIAN_FRONTEND=noninteractive; apt-get -y update && apt-get install -y git-core pandoc pandoc-citeproc libmariadb-client-lgpl-dev libpq-dev make libssl-dev libcurl4-openssl-dev
+R-HUB-R-HUB-R-HUBpwd
+R-HUB-R-HUB-R-HUBdocker run -d --user root --name dplyr_0.8.0.9008.tar.gz-156bd5d47d49482b849cecda2496c4a1-1 -v /home/ubuntu/workspace/dplyr_0.8.0.9008.tar.gz-156bd5d47d49482b849cecda2496c4a1/sysreqs.sh:/root/sysreqs.sh rhub/ubuntu-rchk bash /root/sysreqs.sh
0ade9c30f636a75903a1e72d3c2bf22f0b5ddf7c780f4e4dcf5d8bbbbe95e162
+R-HUB-R-HUB-R-HUBdocker attach dplyr_0.8.0.9008.tar.gz-156bd5d47d49482b849cecda2496c4a1-1
Get:1 http://security.ubuntu.com/ubuntu xenial-security InRelease [109 kB]
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Get:7 http://security.ubuntu.com/ubuntu xenial-security/universe amd64 Packages [545 kB]
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Fetched 3,807 kB in 2s (1,866 kB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
make is already the newest version (4.1-6).
make set to manually installed.
libcurl4-openssl-dev is already the newest version (7.47.0-1ubuntu2.12).
The following additional packages will be installed:
comerr-dev krb5-multidev libbibutils2 libghc-pandoc-citeproc-data libgssrpc4
libkadm5clnt-mit9 libkadm5srv-mit9 libkdb5-8 liblua5.1-0 libluajit-5.1-2
libluajit-5.1-common libmariadb2 libpq5 libssl-doc libyaml-0-2 pandoc-data
Suggested packages:
doc-base krb5-doc krb5-user postgresql-doc-9.5 texlive-xetex texlive-luatex
etoolbox wkhtmltopdf
The following NEW packages will be installed:
comerr-dev git-core krb5-multidev libbibutils2 libghc-pandoc-citeproc-data
libgssrpc4 libkadm5clnt-mit9 libkadm5srv-mit9 libkdb5-8 liblua5.1-0
libluajit-5.1-2 libluajit-5.1-common libmariadb-client-lgpl-dev libmariadb2
libpq-dev libpq5 libssl-dev libssl-doc libyaml-0-2 pandoc pandoc-citeproc
pandoc-data
0 upgraded, 22 newly installed, 0 to remove and 7 not upgraded.
Need to get 16.3 MB of archives.
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Get:4 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libkdb5-8 amd64 1.13.2+dfsg-5ubuntu2.1 [37.0 kB]
Get:5 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libkadm5srv-mit9 amd64 1.13.2+dfsg-5ubuntu2.1 [51.3 kB]
Get:6 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libkadm5clnt-mit9 amd64 1.13.2+dfsg-5ubuntu2.1 [36.6 kB]
Get:7 http://archive.ubuntu.com/ubuntu xenial/main amd64 comerr-dev amd64 2.1-1.42.13-1ubuntu1 [38.2 kB]
Get:8 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 krb5-multidev amd64 1.13.2+dfsg-5ubuntu2.1 [113 kB]
Get:9 http://archive.ubuntu.com/ubuntu xenial/universe amd64 libbibutils2 amd64 4.12-5 [353 kB]
Get:10 http://archive.ubuntu.com/ubuntu xenial/main amd64 liblua5.1-0 amd64 5.1.5-8ubuntu1 [102 kB]
Get:11 http://archive.ubuntu.com/ubuntu xenial/universe amd64 libluajit-5.1-common all 2.0.4+dfsg-1 [35.3 kB]
Get:12 http://archive.ubuntu.com/ubuntu xenial/universe amd64 libluajit-5.1-2 amd64 2.0.4+dfsg-1 [205 kB]
Get:13 http://archive.ubuntu.com/ubuntu xenial/universe amd64 libmariadb2 amd64 2.0.0-1 [108 kB]
Get:14 http://archive.ubuntu.com/ubuntu xenial/universe amd64 libmariadb-client-lgpl-dev amd64 2.0.0-1 [187 kB]
Get:15 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libpq5 amd64 9.5.14-0ubuntu0.16.04 [78.8 kB]
Get:16 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libssl-dev amd64 1.0.2g-1ubuntu4.15 [1,344 kB]
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Get:19 http://archive.ubuntu.com/ubuntu xenial/universe amd64 pandoc-data all 1.16.0.2~dfsg-1 [84.0 kB]
Get:20 http://archive.ubuntu.com/ubuntu xenial/universe amd64 pandoc amd64 1.16.0.2~dfsg-1 [6,601 kB]
Get:21 http://archive.ubuntu.com/ubuntu xenial/universe amd64 libghc-pandoc-citeproc-data all 0.9-1 [49.5 kB]
Get:22 http://archive.ubuntu.com/ubuntu xenial/universe amd64 pandoc-citeproc amd64 0.9-1 [5,493 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Processing triggers for libc-bin (2.23-0ubuntu11) ...
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Setting up git-core (1:2.7.4-0ubuntu1.6) ...
Setting up libgssrpc4:amd64 (1.13.2+dfsg-5ubuntu2.1) ...
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Setting up libkadm5clnt-mit9:amd64 (1.13.2+dfsg-5ubuntu2.1) ...
Setting up comerr-dev (2.1-1.42.13-1ubuntu1) ...
Setting up krb5-multidev (1.13.2+dfsg-5ubuntu2.1) ...
Setting up libbibutils2 (4.12-5) ...
Setting up liblua5.1-0:amd64 (5.1.5-8ubuntu1) ...
Setting up libluajit-5.1-common (2.0.4+dfsg-1) ...
Setting up libluajit-5.1-2:amd64 (2.0.4+dfsg-1) ...
Setting up libmariadb2:amd64 (2.0.0-1) ...
Setting up libmariadb-client-lgpl-dev (2.0.0-1) ...
Setting up libpq5:amd64 (9.5.14-0ubuntu0.16.04) ...
Setting up libssl-dev:amd64 (1.0.2g-1ubuntu4.15) ...
Setting up libpq-dev (9.5.14-0ubuntu0.16.04) ...
Setting up libssl-doc (1.0.2g-1ubuntu4.15) ...
Setting up pandoc-data (1.16.0.2~dfsg-1) ...
Setting up pandoc (1.16.0.2~dfsg-1) ...
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Setting up pandoc-citeproc (0.9-1) ...
Processing triggers for libc-bin (2.23-0ubuntu11) ...
+R-HUB-R-HUB-R-HUBdocker commit dplyr_0.8.0.9008.tar.gz-156bd5d47d49482b849cecda2496c4a1-1
+R-HUB-R-HUB-R-HUBnewimage=sha256:9bd6f227a2f695e23a3f52d9e875cce5c5aeeab51867c43cc0d586bcfc95f77f
+R-HUB-R-HUB-R-HUBtempfile
+R-HUB-R-HUB-R-HUBenv=/tmp/fileomSxtL
+R-HUB-R-HUB-R-HUBecho url=https://builder.r-hub.io/file/0c868f5e9fb048128e648bcd92f0b29e
+R-HUB-R-HUB-R-HUBecho package=dplyr_0.8.0.9008.tar.gz
+R-HUB-R-HUB-R-HUBecho checkArgs=
+R-HUB-R-HUB-R-HUBecho build=false
+R-HUB-R-HUB-R-HUBecho R_REMOTES_STANDALONE=true
+R-HUB-R-HUB-R-HUBecho R_REMOTES_NO_ERRORS_FROM_WARNINGS=true
+R-HUB-R-HUB-R-HUBecho TZ=Europe/London
+R-HUB-R-HUB-R-HUBecho
+R-HUB-R-HUB-R-HUBecho >>>>>==================== Starting Docker container
>>>>>==================== Starting Docker container
+R-HUB-R-HUB-R-HUBpwd
+R-HUB-R-HUB-R-HUBdocker run -i --user docker --env-file /tmp/fileomSxtL -v /home/ubuntu/workspace/dplyr_0.8.0.9008.tar.gz-156bd5d47d49482b849cecda2496c4a1/dplyr_0.8.0.9008.tar.gz:/tmp/dplyr_0.8.0.9008.tar.gz --name dplyr_0.8.0.9008.tar.gz-156bd5d47d49482b849cecda2496c4a1-2 sha256:9bd6f227a2f695e23a3f52d9e875cce5c5aeeab51867c43cc0d586bcfc95f77f /bin/bash -l
/
R Under development (unstable) (2019-03-11 r76221) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> source('https://bioconductor.org/biocLite.R')
Installing package into ‘/opt/R-svn/packages/lib’
(as ‘lib’ is unspecified)
trying URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/BiocInstaller_1.30.0.tar.gz'
Content type 'application/x-gzip' length 19149 bytes (18 KB)
==================================================
downloaded 18 KB
* installing *source* package ‘BiocInstaller’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for help
A newer version of Bioconductor is available for this version of R,
?BiocUpgrade for help
** testing if installed package can be loaded from final location
Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for help
A newer version of Bioconductor is available for this version of R,
?BiocUpgrade for help
** testing if installed package keeps a record of temporary installation path
* DONE (BiocInstaller)
The downloaded source packages are in
‘/tmp/RtmpfnAcny/downloaded_packages’
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A newer version of Bioconductor is available for this version of R,
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>
>
>>>>>==================== Querying package dependencies
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 114k 100 114k 0 0 392k 0 --:--:-- --:--:-- --:--:-- 393k
R Under development (unstable) (2019-03-11 r76221) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
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R is a collaborative project with many contributors.
Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> source("install-github.R")$value("r-lib/remotes@r-hub")
Downloading GitHub repo r-lib/remotes@r-hub
Running `R CMD build`...
* checking for file ‘/tmp/RtmpKTWN5N/remotes5e7b3aca86/r-lib-remotes-8556f2b/DESCRIPTION’ ... OK
* preparing ‘remotes’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘remotes_1.1.1.9000.tar.gz’
Installing package into ‘/opt/R-svn/packages/lib’
(as ‘lib’ is unspecified)
* installing *source* package ‘remotes’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (remotes)
>
>
>>>>>==================== Installing package dependencies
/opt/R-svn/bin:/usr/lib/llvm-4.0/bin:/opt/R-svn/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
/usr/local/bin/wllvm
clang version 4.0.0-1ubuntu1~16.04.2 (tags/RELEASE_400/rc1)
Target: x86_64-pc-linux-gnu
Thread model: posix
InstalledDir: /usr/lib/llvm-4.0/bin
/usr/local/bin/wllvm++ -stdlib=libc++ -std=gnu++11
clang version 4.0.0-1ubuntu1~16.04.2 (tags/RELEASE_400/rc1)
Target: x86_64-pc-linux-gnu
Thread model: posix
InstalledDir: /usr/lib/llvm-4.0/bin
Pandoc:
/usr/bin/pandoc
-rwxr-xr-x 1 root root 53409192 Feb 22 2016 /usr/bin/pandoc
-rwxr-xr-x 1 root root 46913224 Feb 23 2016 /usr/bin/pandoc-citeproc
R Under development (unstable) (2019-03-11 r76221) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> remotes::install_local("dplyr_0.8.0.9008.tar.gz", dependencies = TRUE, INSTALL_opts = "--build")
Error in vapply(remote, function(x) remote_sha(x), character(1), USE.NAMES = FALSE) :
values must be length 1,
but FUN(X[[1]]) result is length 98
Calls: <Anonymous> ... dev_package_deps -> combine_deps -> remote_deps -> vapply
Execution halted
> library(dplyr)
Error in library(dplyr) : there is no package called ‘dplyr’
Execution halted
Build step 'Execute shell' marked build as failure
Pinging https://builder.r-hub.io/build/FAILURE/dplyr_0.8.0.9008.tar.gz-156bd5d47d49482b849cecda2496c4a1/2019-03-14T06:14:49Z
{"status":"ok"}
Finished: FAILURE
romainfrancois commented
Without the remote, I do get the usual ERROR, which is expected at this point:
https://builder.r-hub.io/status/original/dplyr_0.8.0.9008.tar.gz-b0fe138d29b3409ea9171b6b1c3b6ac5
gaborcsardi commented
I can reproduce it, seems like a remotes bug.
gaborcsardi commented
> remotes::install_local("dplyr_0.8.0.9008.tar.gz", dependencies = TRUE, INSTALL_opts = "--build")
Error in vapply(remote, function(x) remote_sha(x), character(1), USE.NAMES = FALSE) :
values must be length 1,
but FUN(X[[1]]) result is length 98
> traceback()
10: vapply(remote, function(x) remote_sha(x), character(1), USE.NAMES = FALSE)
9: remote_deps(pkg, ...)
8: combine_deps(package_deps(deps, repos = repos, type = type),
remote_deps(pkg, ...))
7: dev_package_deps(pkgdir, repos = repos, dependencies = dependencies,
type = type, ...)
6: install_deps(pkgdir, dependencies = dependencies, quiet = quiet,
build = build, build_opts = build_opts, repos = repos, type = type,
...)
5: install(source, dependencies = dependencies, upgrade = upgrade,
force = force, quiet = quiet, build = build, build_opts = build_opts,
repos = repos, type = type, ...)
4: FUN(X[[i]], ...)
3: vapply(remotes, install_remote, ..., FUN.VALUE = character(1))
2: install_remotes(remotes, dependencies = dependencies, upgrade = upgrade,
force = force, quiet = quiet, build = build, build_opts = build_opts,
repos = repos, type = type, ...)
1: remotes::install_local("dplyr_0.8.0.9008.tar.gz", dependencies = TRUE,
INSTALL_opts = "--build")
gaborcsardi commented
Should be fixed in r-lib/remotes@c2cdc74