Both package 'ggpubr' and 'rstatix' depend on package 'nloptr'. Since the latest update of 'nloptr' (Around May 5th if I remembered correctly), I can't update my shinyapp anymore. And I tried with another small reprex that used 'ggpubr' package, which also failed with "ERROR: configuration failed for package 'nloptr'".
Here is a small reprex:
library(ggpubr)
library(shiny)
data("iris")
## ui file
ui <- fluidPage(
plotOutput('barplot')
)
## server file
server <- function(input, output, session) {
data(iris)
barplot1 <- reactive({
ggbarplot(data = iris, y='Sepal.Length', x='Species',
add = 'mean_sd', fill = 'Species' ) +
stat_compare_means(method = 't.test',
ref.group = 'setosa',
label = 'p.signif', hide.ns = T)
})
output$barplot <- renderPlot(barplot1())
}
The error basically indicated that cmake is not found.
Uploading bundle for application: 6265085...DONE
Deploying bundle: 5893926 for application: 6265085 ...
Waiting for task: 1151049668
building: Building image: 6883839
building: Fetching packages
building: Building package: nloptr
################################ Begin Task Log ################################
...
checking for cmake... no
------------------ CMAKE NOT FOUND --------------------
CMake was not found on the PATH. Please install CMake
...
ERROR: configuration failed for package nloptr
* removing /opt/R/4.1.2/lib/R/library/nloptr
################################# End Task Log #################################
Error: Unhandled Exception: Child Task 1151049670 failed: Error building image: Error building nloptr (2.0.1). Build exited with non-zero status: 1
But I thought shinyapp.io had preinstalled cmake before app deployment? I don't know what happened. Please offer me some help here, thanks.
1 Like
This relates to your system not shinyapps.io's system
Package updates take a while to get into the package cache (RStudio Package Manager), shinyapps.io doesn't work very well when packages need to be compiled so either wait for the new version to be cached or install an older version meanwhile. If you install an older version in your system, rsconnect is going to replicate your environment on shinyapps.io.
I'm having the same issue (though it seems to be different, though)..
################################ Begin Task Log ################################
GET /v1/tasks/1176870721/logs/ 390ms
GET /v1/tasks/?filter=account_id:1318953&filter=parent_id:1176870721&count=100&offset=0 400ms
GET /v1/tasks/1176870722/logs/ 590ms
[2022-06-27T11:58:52.893501071+0000] Execute script: packages/build/gmp.sh
- set -e
++ lsb_release -cs
- OS_CODENAME=focal
- apt-get update -qq
- '[' focal == xenial ']'
- apt-get install -y libgmp-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
libgmpxx4ldbl
Suggested packages:
gmp-doc libgmp10-doc libmpfr-dev
The following NEW packages will be installed:
libgmp-dev libgmpxx4ldbl
0 upgraded, 2 newly installed, 0 to remove and 31 not upgraded.
Need to get 330 kB of archives.
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Get:2 Index of /ubuntu focal/main amd64 libgmp-dev amd64 2:6.2.0+dfsg-4 [320 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package libgmp-dev:amd64.
Preparing to unpack .../libgmp-dev_2%3a6.2.0+dfsg-4_amd64.deb ...
Unpacking libgmp-dev:amd64 (2:6.2.0+dfsg-4) ...
Setting up libgmpxx4ldbl:amd64 (2:6.2.0+dfsg-4) ...
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Processing triggers for libc-bin (2.31-0ubuntu9.7) ...
[2022-06-27T11:58:56.567627752+0000] Execute script: packages/build/hunspell.sh
- set -e
- apt-get update -qq
- apt-get install -y libhunspell-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
dictionaries-common emacsen-common hunspell-en-us libhunspell-1.7-0
Suggested packages:
ispell | aspell | hunspell wordlist hunspell openoffice.org-hunspell
| openoffice.org-core
The following NEW packages will be installed:
dictionaries-common emacsen-common hunspell-en-us libhunspell-1.7-0
libhunspell-dev
0 upgraded, 5 newly installed, 0 to remove and 31 not upgraded.
Need to get 707 kB of archives.
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Get:1 Index of /ubuntu focal/main amd64 emacsen-common all 3.0.4 [14.9 kB]
Get:2 Index of /ubuntu focal/main amd64 dictionaries-common all 1.28.1 [178 kB]
Get:3 Index of /ubuntu focal/main amd64 hunspell-en-us all 1:2018.04.16-1 [170 kB]
Get:4 Index of /ubuntu focal/main amd64 libhunspell-1.7-0 amd64 1.7.0-2build2 [147 kB]
Get:5 Index of /ubuntu focal/main amd64 libhunspell-dev amd64 1.7.0-2build2 [197 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 707 kB in 0s (13.3 MB/s)
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Adding 'diversion of /usr/share/dict/words to /usr/share/dict/words.pre-dictionaries-common by dictionaries-common'
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Preparing to unpack .../libhunspell-dev_1.7.0-2build2_amd64.deb ...
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Setting up dictionaries-common (1.28.1) ...
debconf: unable to initialize frontend: Dialog
debconf: (TERM is not set, so the dialog frontend is not usable.)
debconf: falling back to frontend: Readline
Setting up hunspell-en-us (1:2018.04.16-1) ...
Processing triggers for libc-bin (2.31-0ubuntu9.7) ...
Processing triggers for dictionaries-common (1.28.1) ...
debconf: unable to initialize frontend: Dialog
debconf: (TERM is not set, so the dialog frontend is not usable.)
debconf: falling back to frontend: Readline
[2022-06-27T11:59:00.693662056+0000] Execute script: packages/build/Rmpfr.sh
- set -e
- apt-get update -qq
- apt-get install -y libmpfr-dev
Reading package lists...
Building dependency tree...
Reading state information...
Suggested packages:
libmpfr-doc
The following NEW packages will be installed:
libmpfr-dev
0 upgraded, 1 newly installed, 0 to remove and 31 not upgraded.
Need to get 240 kB of archives.
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Get:1 Index of /ubuntu focal/main amd64 libmpfr-dev amd64 4.0.2-1 [240 kB]
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[2022-06-27T11:59:03.761477002+0000] Execute script: packages/build/tm.sh
- set -e
- apt-get update -qq
- apt-get install -y antiword poppler-utils
Reading package lists...
Building dependency tree...
Reading state information...
The following NEW packages will be installed:
antiword poppler-utils
0 upgraded, 2 newly installed, 0 to remove and 31 not upgraded.
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Get:2 Index of /ubuntu focal/main amd64 poppler-utils amd64 0.86.1-0ubuntu1 [174 kB]
debconf: delaying package configuration, since apt-utils is not installed
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[2022-06-27T11:59:06.812449736+0000] Execute script: packages/build/igraph.sh
- set -e
- apt-get update -qq
- apt-get install -y libglpk-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
libamd2 libbtf1 libcamd2 libccolamd2 libcholmod3 libcolamd2 libcxsparse3
libglpk40 libgraphblas3 libklu1 libldl2 libmetis5 libmongoose2 librbio2
libspqr2 libsuitesparse-dev libsuitesparseconfig5 libumfpack5
Suggested packages:
libiodbc2-dev
The following NEW packages will be installed:
libamd2 libbtf1 libcamd2 libccolamd2 libcholmod3 libcolamd2 libcxsparse3
libglpk-dev libglpk40 libgraphblas3 libklu1 libldl2 libmetis5 libmongoose2
librbio2 libspqr2 libsuitesparse-dev libsuitesparseconfig5 libumfpack5
0 upgraded, 19 newly installed, 0 to remove and 31 not upgraded.
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Get:4 Index of /ubuntu focal/main amd64 libcamd2 amd64 1:5.7.1+dfsg-2 [21.7 kB]
Get:5 Index of /ubuntu focal/main amd64 libccolamd2 amd64 1:5.7.1+dfsg-2 [23.2 kB]
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Get:7 Index of /ubuntu focal/main amd64 libmetis5 amd64 5.1.0.dfsg-5 [169 kB]
Get:8 Index of /ubuntu focal/main amd64 libcholmod3 amd64 1:5.7.1+dfsg-2 [308 kB]
Get:9 Index of /ubuntu focal/main amd64 libcxsparse3 amd64 1:5.7.1+dfsg-2 [64.2 kB]
Get:10 Index of /ubuntu focal/universe amd64 libglpk40 amd64 4.65-2 [378 kB]
Get:11 Index of /ubuntu focal/main amd64 libgraphblas3 amd64 1:5.7.1+dfsg-2 [3770 kB]
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Setting up librbio2:amd64 (1:5.7.1+dfsg-2) ...
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Setting up libcamd2:amd64 (1:5.7.1+dfsg-2) ...
Setting up libmongoose2:amd64 (1:5.7.1+dfsg-2) ...
Setting up libglpk40:amd64 (4.65-2) ...
Setting up libklu1:amd64 (1:5.7.1+dfsg-2) ...
Setting up libccolamd2:amd64 (1:5.7.1+dfsg-2) ...
Setting up libcholmod3:amd64 (1:5.7.1+dfsg-2) ...
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Processing triggers for libc-bin (2.31-0ubuntu9.7) ...
[2022-06-27T11:59:19.647626117+0000] Installing R package: BH (1.78.0-0)
- installing to library '/opt/R/4.1.2/lib/R/library'
- installing binary package 'BH' ...
- DONE (BH)
[2022-06-27T11:59:32.027059341+0000] Installing R package: ISOcodes (2022.01.10)
- installing to library '/opt/R/4.1.2/lib/R/library'
- installing binary package 'ISOcodes' ...
- DONE (ISOcodes)
[2022-06-27T11:59:32.367240262+0000] Installing R package: KernSmooth (2.23-20)
- installing to library '/opt/R/4.1.2/lib/R/library'
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[2022-06-27T11:59:32.717379677+0000] Installing R package: MASS (7.3-57)
- installing to library '/opt/R/4.1.2/lib/R/library'
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- DONE (MASS)
[2022-06-27T11:59:33.130540795+0000] Installing R package: NLP (0.2-1)
- installing to library '/opt/R/4.1.2/lib/R/library'
- installing binary package 'NLP' ...
- DONE (NLP)
[2022-06-27T11:59:33.470576435+0000] Installing R package: R6 (2.5.1)
- installing to library '/opt/R/4.1.2/lib/R/library'
- installing binary package 'R6' ...
- DONE (R6)
[2022-06-27T11:59:33.795020854+0000] Installing R package: RColorBrewer (1.1-3)
- installing to library '/opt/R/4.1.2/lib/R/library'
- installing binary package 'RColorBrewer' ...
- DONE (RColorBrewer)
[2022-06-27T11:59:34.127319525+0000] Installing R package: Rcpp (1.0.8.3)
- installing to library '/opt/R/4.1.2/lib/R/library'
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[2022-06-27T11:59:35.375680185+0000] Installing R package: SQUAREM (2021.1)
- installing to library '/opt/R/4.1.2/lib/R/library'
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(...)
[2022-06-27T12:01:18.624995744+0000] Installing R package: recipes (0.2.0)
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[2022-06-27T12:01:19.034364743+0000] Installing R package: rsample (1.0.0)
- installing to library '/opt/R/4.1.2/lib/R/library'
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[2022-06-27T12:01:19.403210094+0000] Installing R package: statsExpressions (1.3.2)
- installing to library '/opt/R/4.1.2/lib/R/library'
- installing binary package 'statsExpressions' ...
- DONE (statsExpressions)
[2022-06-27T12:01:19.906968574+0000] Installing R package: inspectdf (0.0.11)
- installing to library '/opt/R/4.1.2/lib/R/library'
- installing binary package 'inspectdf' ...
- DONE (inspectdf)
[2022-06-27T12:01:20.310471530+0GET /v1/tasks/?filter=account_id:1318953&filter=parent_id:1176870722&count=100&offset=0 420ms
################################# End Task Log #################################
----- Deployment error -----
Fehler: Unhandled Exception: Child Task 1176870722 failed: Error building image: Error building nloptr (2.0.3). Build exited with non-zero status: 1
----- Error stack trace -----
4: rsconnect::deployApp(appDir = "C:/Users/User/OneDrive/Desktop/Datenanalyse/Error analysis/Saved",
appFileManifest = "C:/Users/User~1/AppData/Local/Temp/622c-0615-f60a-f241",
appPrimaryDoc = "error.Rmd", appSourceDoc = "C:/Users/User/OneDrive/Desktop/Datenanalyse/Error analysis/Saved/error.Rmd",
...
3: client$waitForTask(taskId, quiet)
2: stop(status$error, call. = FALSE)
1: (function (e)
{
cat("----- Deployment error -----\n")
...
Error: Unhandled Exception: Child Task 1176870722 failed: Error building image: Error building nloptr (2.0.3). Build exited with non-zero status: 1
Execution stopped
According to Install cmake when nloptr is a dependency · Issue #328 · rstudio/shinyapps-package-dependencies · GitHub a fix has been rolled out so there is a chance that the nloptr issues are fixed now.
And - if nothing works and you just need "a" version of nloptr - downgrading to version 1.x of nloptr (prior of publishing to shinyapps.io) will always fix any compilation issue with nloptr, cf. other post on this topic Installing package nloptr