Question: org.Hs.eg.db can not be downloaded
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Entering edit mode
@liuzhizheng1996-23805
Last seen 14 months ago

Hi,I am getting troubles in downloading org.Hs.eg.db package by R software type 4.0.0. The discriptions were displayed below. I wil be appreciated if you could answer me! Thanks a lot!


>   #install 'DBI', "AnnotationDbi"packages
BiocManager::install(c('DBI', "AnnotationDbi"))
Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.0 (2020-04-24)
Installing package(s) 'DBI', 'AnnotationDbi'
试开URL’https://cran.rstudio.com/bin/windows/contrib/4.0/DBI_1.1.0.zip'
Content type 'application/zip' length 662734 bytes (647 KB)
downloaded 647 KB

试开URL’https://bioconductor.org/packages/3.11/bioc/bin/windows/contrib/4.0/AnnotationDbi_1.50.1.zip'
Content type 'application/zip' length 5250195 bytes (5.0 MB)
downloaded 5.0 MB

package ‘DBI’ successfully unpacked and MD5 sums checked
package ‘AnnotationDbi’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\Dr.liu\AppData\Local\Temp\Rtmp4IYCX4\downloaded_packages
Old packages: 'boot', 'class', 'foreign', 'KernSmooth', 'MASS', 'nlme', 'nnet', 'spatial', 'survival'
Update all/some/none? [a/s/n]: 
n


 #install "org.Hs.eg.db" package
> BiocManager::install("org.Hs.eg.db")
Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.0 (2020-04-24)
Installing package(s) 'org.Hs.eg.db'
installing the source package ‘org.Hs.eg.db’

试开URL’https://bioconductor.org/packages/3.11/data/annotation/src/contrib/org.Hs.eg.db_3.11.4.tar.gz'
Content type 'application/x-gzip' length 79959831 bytes (76.3 MB)
downloaded 8.5 MB

Error in untar2(tarfile, files, list, exdir, restore_times) : 
  incomplete block on file

The downloaded source packages are in
    ‘C:\Users\Dr.liu\AppData\Local\Temp\Rtmp4IYCX4\downloaded_packages’
Old packages: 'boot', 'class', 'foreign', 'KernSmooth', 'MASS', 'nlme', 'nnet', 'spatial', 'survival'
Update all/some/none? [a/s/n]: 
n
Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 8908800 != reported length 79959831
2: In install.packages(...) :
  installation of package ‘org.Hs.eg.db’ had non-zero exit status
software error • 398 views
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Thank you for all the help,finally i installed the package successfully.Though,The reason remains unclear. I uninstalled all the relevant packages and downloaded relevant packages from the website.

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1
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Guido Hooiveld ★ 3.0k
@guido-hooiveld-2020
Last seen 1 day ago
Wageningen University, Wageningen, the …

This seems to be due to a corrupted download.

Notice:

Error in untar2(tarfile, files, list, exdir, restore_times) : 
  incomplete block on file

and also note that there is a length problem.:

1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 8908800 != reported length 79959831

So please try again. Confirm, though, that you have sufficient HDD space (also at the temp location).

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0
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Thank you for your prompt reply.But i have tried it for several times, it still doesn't work. I am sure there is enough HD space on my computer. I also tried to download "org.Hs.eg.db" package from website, and install it from local disk by R. The package failed to install. The descriptions are displayed below:

install.packages("D:/test/org.Hs.eg.db_3.11.4.tar.gz", repos = NULL, type = "source")
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:

https://cran.rstudio.com/bin/windows/Rtools/
* installing *source* package 'org.Hs.eg.db' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package or namespace load failed for 'AnnotationDbi' in inDL(x, as.logical(local), as.logical(now), ...):
 无法载入共享目标对象‘D:/study software/R-4.0.0/library/Rcpp/libs/i386/Rcpp.dll’::
  LoadLibrary failure:  找不到指定的程序。

错误: 无法载入程辑包'AnnotationDbi'
停止执行
ERROR: lazy loading failed for package 'org.Hs.eg.db'
* removing 'D:/study software/R-4.0.0/library/org.Hs.eg.db'
Warning in install.packages :
  installation of package ‘D:/test/org.Hs.eg.db_3.11.4.tar.gz’ had non-zero exit status

"无法载入共享目标对象‘D:/study software/R-4.0.0/library/Rcpp/libs/i386/Rcpp.dll’:: LoadLibrary failure: 找不到指定的程序。 错误: 无法载入程辑包'AnnotationDbi' 停止执行" mean error in loading targeted object:‘D:/study software/R-4.0.0/library/Rcpp/libs/i386/Rcpp.dll’ LoadLibrary failure: The program could not be found error in loading 'AnnotationDbi'

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Entering edit mode

Please note that the recommended way to install packages is using BiocManager, not install.packages.

Moreover, you try to install a package from source. Since you are on Windows, you need to have installed Rtools first. Link is here.

Finally, because you are installing from source using install.packages() the required package dependencies are not automatically take care of. [using BiocManager does!]

Having said this, please try the following: BiocManager::install("AnnotationDbi") # because of error message in your 2nd post. BiocManager::install("org.Hs.eg.db") # or install from source after having installed Rtools and AnnotationDbi.

Lastly, I noticed you would like to install packages in D:/study software/R-4.0.0/xxxx. There is a space between study and software, which I always try to prevent (although I don't know whether this still causes complications with R on Windows).

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