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

installation error #56

Closed
englianhu opened this issue Jun 13, 2021 · 3 comments
Closed

installation error #56

englianhu opened this issue Jun 13, 2021 · 3 comments

Comments

@englianhu
Copy link

englianhu commented Jun 13, 2021 •
edited
Loading 

#install.packages("BiocManager")
BiocManager::install("EBImage")
...
...
installing to /usr/lib/R/library/00LOCK-EBImage/00new/EBImage/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Error in namespaceExport(ns, exports) : undefined exports: class AsIs
Calls: <Anonymous> ... namespaceImportFrom -> asNamespace -> loadNamespace -> namespaceExport
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘EBImage’ in namespaceExport(ns, exports):
 undefined exports: class AsIs
Error: loading failed
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Error: package or namespace load failed for ‘EBImage’ in namespaceExport(ns, exports):
 undefined exports: class AsIs
Error: loading failed
Error in namespaceExport(ns, exports) : undefined exports: class AsIs
Calls: <Anonymous> ... namespaceImportFrom -> asNamespace -> loadNamespace -> namespaceExport
** testing if installed package keeps a record of temporary installation path
* DONE (EBImage)

http://bioconductor.org/packages/devel/bioc/vignettes/EBImage/inst/doc/EBImage-introduction.html

✓ [master*]> library(EBImage)
ℹ EBImage not installed. Trying to install now
Install 'aoles/EBImage'? (Y/N): 
R-project: EBImage (Documents/GitHub/EBImage)
Y
...
...
...
installing to /usr/lib/R/library/00LOCK-EBImage/00new/EBImage/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Error in namespaceExport(ns, exports) : undefined exports: class AsIs
Calls: <Anonymous> ... namespaceImportFrom -> asNamespace -> loadNamespace -> namespaceExport
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘EBImage’ in namespaceExport(ns, exports):
 undefined exports: class AsIs
Error: loading failed
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Error: package or namespace load failed for ‘EBImage’ in namespaceExport(ns, exports):
 undefined exports: class AsIs
Error: loading failed
Error in namespaceExport(ns, exports) : undefined exports: class AsIs
Calls: <Anonymous> ... namespaceImportFrom -> asNamespace -> loadNamespace -> namespaceExport
** testing if installed package keeps a record of temporary installation path
* DONE (EBImage)
Error: package or namespace load failed for 'EBImage' in namespaceExport(ns, exports):
 undefined exports: class AsIs
✓ [master*]> BBmisc::lib('EBImage')
Loading required package: EBImage
Error: package or namespace load failed for 'EBImage' in namespaceExport(ns, exports):
 undefined exports: class AsIs
Installing package into '/usr/lib/R/library'
(as 'lib' is unspecified)
Loading required package: EBImage
Error: package or namespace load failed for 'EBImage' in namespaceExport(ns, exports):
 undefined exports: class AsIs
Warning message:
package 'EBImage' is not available for this version of R

A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages 
EBImage 
  FALSE

ropensci/magick#320 (comment) doesn't help...
@englianhu
Copy link
Author 

:~$ sudo su - -c "R -e \"devtools::install_github('aoles/EBImage', dependencies=TRUE, force=TRUE)\""

R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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.

> devtools::install_github('aoles/EBImage', dependencies=TRUE, force=TRUE)
Downloading GitHub repo aoles/EBImage@HEAD
BiocStyle (NA -> 2.22.0) [CRAN]
Installing 1 packages: BiocStyle
trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/BiocStyle_2.22.0.tar.gz'
Content type 'application/x-gzip' length 756743 bytes (739 KB)
==================================================
downloaded 739 KB

* installing *source* package ‘BiocStyle’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** 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 (BiocStyle)

The downloaded source packages are in
        ‘/tmp/RtmpjRcQbs/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
✔  checking for file ‘/tmp/RtmpjRcQbs/remoteseec950521bf6/aoles-EBImage-d418e72/DESCRIPTION’ ...
─  preparing ‘EBImage’:
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘EBImage_4.35.2.tar.gz’
   
* installing *source* package ‘EBImage’ ...
** using staged installation
** libs
gcc -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-lENDSu/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c EBImage.c -o EBImage.o
gcc -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-lENDSu/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c clahe.c -o clahe.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-lENDSu/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c distmap.cpp -o distmap.o
gcc -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-lENDSu/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c drawCircle.c -o drawCircle.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-lENDSu/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c floodFill.cpp -o floodFill.o
gcc -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-lENDSu/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c getFrames.c -o getFrames.o
gcc -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-lENDSu/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c haralick.c -o haralick.o
gcc -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-lENDSu/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c medianFilter.c -o medianFilter.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-lENDSu/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c morphology.cpp -o morphology.o
gcc -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-lENDSu/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c nativeRaster.c -o nativeRaster.o
gcc -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-lENDSu/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c normalize.c -o normalize.o
gcc -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-lENDSu/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c objects.c -o objects.o
gcc -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-lENDSu/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ocontour.c -o ocontour.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-lENDSu/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c propagate.cpp -o propagate.o
gcc -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-lENDSu/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c spatial.c -o spatial.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-lENDSu/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c thresh.cpp -o thresh.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-lENDSu/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c tile.cpp -o tile.o
gcc -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-lENDSu/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c tools.c -o tools.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-lENDSu/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c transpose.cpp -o transpose.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-lENDSu/r-base-4.1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c watershed.cpp -o watershed.o
g++ -std=gnu++14 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o EBImage.so EBImage.o clahe.o distmap.o drawCircle.o floodFill.o getFrames.o haralick.o medianFilter.o morphology.o nativeRaster.o normalize.o objects.o ocontour.o propagate.o spatial.o thresh.o tile.o tools.o transpose.o watershed.o -L/usr/lib/R/lib -lR
installing to /usr/lib/R/library/00LOCK-EBImage/00new/EBImage/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Error in completeSubclasses(classDef2, class1, obj, where) : 
  trying to get slot "subclasses" from an object of a basic class ("NULL") with no slots
Error: package or namespace load failed for ‘dbplyr’:
 .onLoad failed in loadNamespace() for 'dbplyr', details:
  call: setClass(cl, contains = c(prevClass, "VIRTUAL"), where = where)
  error: error in contained classes ("character") for class “ident”; class definition removed from ‘dbplyr’
Error in .requirePackage(package) : 
  unable to find required package ‘dbplyr’
Calls: <Anonymous> ... .recacheSubclasses -> getClassDef -> .requirePackage
Execution halted
ERROR: lazy loading failed for package ‘EBImage’
* removing ‘/usr/lib/R/library/EBImage’
Warning message:
In i.p(...) :
  installation of package ‘/tmp/RtmpjRcQbs/fileeec97f79dbb/EBImage_4.35.2.tar.gz’ had non-zero exit status

@englianhu
Copy link
Author

通过终端后台安装即可（Translate: install through terminal will do）。

sudo su - -c "R -e \"install.packages(c('BiocManager'), repos='https://cran.rstudio.org', lib='/usr/lib/R/library', dependencies = TRUE, INSTALL_opts = '--no-lock')\""

或者（translte: or）

:~$ sudo su - -c "R -e \"BBmisc::lib('BiocManager')\""

R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 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.

> BBmisc::lib('BiocManager')
Loading required package: BiocManager
BiocManager 
       TRUE

This was referenced Jun 6, 2022
Closed
Closed
Open
Closed
@englianhu
Copy link
Author

englianhu commented Aug 29, 2022 •
edited
Loading

Installation of EBImage on 🚩🇨🇳🏹中科红旗 RedFlag Linux (🍥Debian 11)

sudo su - -c "R -e \"devtools::install_github('aoles/EBImage')\"" working fine with 🚩🇨🇳🏹中科红旗 RedFlag Linux

@englianhu englianhu mentioned this issue Aug 30, 2022
Closed
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
1 participant
@englianhu