.onLoad failed in loadNamespace() for 'org.Hs.eg.db'
3
16
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Arun ▴ 160
@a3151529
Last seen 3.6 years ago
United States

I am trying to install and load the pathview (1.31.2) package, but it fails to load with the error below. I have RQSLite 2.2.6 and org.Hs.eq.db 3.12.0. Could you please help me out ?


> library(pathview)
Error: package or namespace load failed for ‘pathview’:
 .onLoad failed in loadNamespace() for 'org.Hs.eg.db', details:
  call: l$contains
  error: $ operator is invalid for atomic vectors


> sessionInfo( )
R version 4.0.5 (2021-03-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.18.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8      
 [8] LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] AnnotationDbi_1.52.0 IRanges_2.24.1       S4Vectors_0.28.1     Biobase_2.50.0       BiocGenerics_0.36.0 

loaded via a namespace (and not attached):
 [1] KEGGgraph_1.50.0    Rcpp_1.0.6          tidyr_1.1.3         png_0.1-7           Biostrings_2.58.0   assertthat_0.2.1    digest_0.6.27       utf8_1.2.1          R6_2.5.0           
[10] RSQLite_2.2.6       evaluate_0.14       httr_1.4.2          ggplot2_3.3.3       pillar_1.5.1        zlibbioc_1.36.0     rlang_0.4.10        lazyeval_0.2.2      rstudioapi_0.13    
[19] data.table_1.14.0   Rgraphviz_2.34.0    blob_1.2.1          rmarkdown_2.7       htmlwidgets_1.5.3   RCurl_1.98-1.3      bit_4.0.4           munsell_0.5.0       tinytex_0.31       
[28] compiler_4.0.5      xfun_0.22           pkgconfig_2.0.3     htmltools_0.5.1.1   tidyselect_1.1.0    KEGGREST_1.30.1     tibble_3.1.0        XML_3.99-0.6        fansi_0.4.2        
[37] viridisLite_0.3.0   crayon_1.4.1        dplyr_1.0.5         bitops_1.0-6        grid_4.0.5          jsonlite_1.7.2      gtable_0.3.0        lifecycle_1.0.0     DBI_1.1.1          
[46] magrittr_2.0.1      scales_1.1.1        graph_1.68.0        cachem_1.0.4        XVector_0.30.0      ellipsis_0.3.1      generics_0.1.0      vctrs_0.3.7         RColorBrewer_1.1-2 
[55] tools_4.0.5         Cairo_1.5-12.2      bit64_4.0.5         glue_1.4.2          purrr_0.3.4         fastmap_1.1.0       yaml_2.2.1          colorspace_2.0-0    BiocManager_1.30.12
[64] memoise_2.0.0       plotly_4.9.3        knitr_1.31 

> BiocManager::valid()
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cloud.r-project.org

[1] TRUE

Thanks,

Arun
org.Hs.eg.db pathview • 12k views
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2
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I'm experiencing the same issue with org.Hs.eg.db I've the same configuration and version of packages, however running under Ubuntu 20.04.2 LTS

Installation via BiocManager::install("org.Hs.eg.db") goes fine, however when loading the package with library("org.Hs.eg.db") it gives the same error as yours.

I'll follow the updates to this issue.

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1
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I have the same issue with loading org.Hs.eg.db package. The error was as follow

Error: package or namespace load failed for ‘org.Hs.eg.db’: .onLoad failed in loadNamespace() for 'org.Hs.eg.db', details: call: l$contains error: $ operator is invalid for atomic vectors

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1
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I have the same problem. I can install org.Hs.eg.db and but not load ... with RStudio. If I run the code in terminal yes I can do it.

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0
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Yeah, same for me! On terminal everithing is fine, not with RStudio

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0
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It's not a solution, but to be able to generate reports with RMD, I run the script with system ("Script.R"), and load the results

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0
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I am experiencing the same problem. My script run fine till yesterday with no issues installing packages and libraries. Today I am using RMD to write a report for an enrichment analysis and I am stuck activating the org.Hs.eg.db" library. I got in return the message:

"Error: package or namespace load failed for ‘org.Hs.eg.db’: .onLoad failed in loadNamespace() for 'org.Hs.eg.db', details: call: l$contains error: $ operator is invalid for atomic vectors"

It seems an ongoing present generalized issue as I get the same issue even if I run the command library("org.Hs.eg.db") a separate script today!!!

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0
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I am having the same issue, my code was working, I went to lunch and now it's not. The pathview, org.Mm.eg.db, and org.Hs.eg.db packages won't load. All give the error:

Error: package or namespace load failed for ‘pathview’: .onLoad failed in loadNamespace() for 'org.Hs.eg.db', details: call: l$contains error: $ operator is invalid for atomic vectors

Any solutions?

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1
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I have a similar issue (MacOS 10.15.7), for both Hs and Mm eg.db packages. I have reinstalled R and all libraries, the error persists.

My deets:

> library(org.Mm.eg.db)
Error: package or namespace load failed for ‘org.Mm.eg.db’:
 .onLoad failed in loadNamespace() for 'org.Mm.eg.db', details:
  call: l$contains
  error: $ operator is invalid for atomic vectors
> sessionInfo()
R version 4.0.5 (2021-03-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/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  stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
[1] AnnotationDbi_1.52.0 IRanges_2.24.1       S4Vectors_0.28.1    
[4] Biobase_2.50.0       BiocGenerics_0.36.0 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.6          DBI_1.1.1           RSQLite_2.2.6      
 [4] cachem_1.0.4        rlang_0.4.10        blob_1.2.1         
 [7] vctrs_0.3.7         tools_4.0.5         bit64_4.0.5        
[10] bit_4.0.4           fastmap_1.1.0       compiler_4.0.5     
[13] pkgconfig_2.0.3     BiocManager_1.30.12 memoise_2.0.0

org.Mm.eg.db installed without an error.

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0
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Same issue facing:

RA_processed <- input_processing(input = RA_input, # the input: in this case, differential expression results

  • p_val_threshold = 0.05, # p value threshold to filter significant genes
  • pin_name_path = "Biogrid", # the name of the PIN to use for active subnetwork search
  • convert2alias = TRUE) Number of genes provided in input: 572 Number of genes in input after p-value filtering: 572 Error: .onLoad failed in loadNamespace() for 'org.Hs.eg.db', details: call: l$contains error: $ operator is invalid for atomic vectors
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1
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I'm experiencing the same error. I also downloaded the source package (from https://bioconductor.org/packages/release/data/annotation/html/org.Hs.eg.db.html) and installed in Rstudio with no errors. When loading the library returns the same error as yours:

library("org.Hs.eg.db")
Error: package or namespace load failed for ‘org.Hs.eg.db’:
 .onLoad failed in loadNamespace() for 'org.Hs.eg.db', details:
  call: l$contains
  error: $ operator is invalid for atomic vectors

I was using this library just over the weekend with no problems. Maybe there's an issue with the latest version of the library?

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1
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i have same problem.. Nothing is working.... i have tried everything!!

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0
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I can't see org.Hs.eg.db installed, retry BiocManager::install("org.Hs.eg.db") ?

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0
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Also having this issue (R 4.0.3) with org.Mm.eg.db as of today. All was working fine yesterday. I have updated a few packages this morning which may have caused the issue. I have also been connecting to GO.db perhaps there's some sort of conflict?

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1
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Could be, it also worked for me in the recent past. FYI, I tried to install an older version of R (3.6.1) & org.Mm.eg.db in a conda env and run Rstudio from the env. Still the same package loading error.

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0
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However, using conda-installed RStudio helped (see below).

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12
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Kevin Ushey ▴ 130
@kevin-ushey-5913
Last seen 3.6 years ago
United States

This appears to be a bug in the communication between the latest release of the RSQLite package and RStudio. In the interim, you can run:

options(connectionObserver = NULL)

in your RStudio R session before attempting to load these packages (or, use a package that makes a connection via RSQLite).

You can also install the previous release of RSQLite using remotes, e.g. with:

remotes::install_version("RSQLite", version = "2.2.5")

Sorry for the trouble -- we'll try to get this fixed ASAP. :-/
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2
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I am glad to see that this is an RStudio issue and not a me issue! I thought I had gone crazy.

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0
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i have the same issue, and I thought i had gone crazy.

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0
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This didn't work for me, I still get the same error.

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0
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Restart R. This ultimately worked for me (specifically the rollback of RSQLite), but it's a temporary fix in either case.

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0
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i tried restarting and it still didn't work.

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0
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Restarting works for me.

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0
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Thank you for your proposal to solve the problem! This method solved my problem very well, but the code has a spelling error and should be changed into options(connectionObserver = NULL). Initially, I copied your code and found that it didn't solve the problem. It turned out to be the spelling error of the code. I hope my experience can be useful to others.

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0
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Ack, thank you for catching that! I've updated my post.

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3
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泉剑 ▴ 30
@4524930d
Last seen 3.6 years ago
Taiwan

The strange thing is that when I use terminal R to load org.Hs.eg.db it can be loaded well If you are in a hurry to use it, this might be a help
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2
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This error is now also filed as an issue in RStudio: Issue with annotation database connection only in RStudio

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1
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Please resolve this issue as soon as possible.

Rstudio is still generating error during loading of org.Hs.eg.db package

library("org.Hs.eg.db") Error: package or namespace load failed for ‘org.Hs.eg.db’: .onLoad failed in loadNamespace() for 'org.Hs.eg.db', details: call: l$contains error: $ operator is invalid for atomic vectors

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0
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agata ▴ 20
@ef52dc19
Last seen 3.5 years ago
Sweden

This is not The Solution, but it may help some people who need org.Nn.eg.db now and would like to continue working in RStudio.

I created a conda environment:

# install mamba, a faster env solver than conda in your base conda env
conda install mamba -n base -c conda-forge

conda create -n R-orgMm
conda activate R-orgMm

mamba install -c r r-essentials r-base=3.6.1
mamba install -c bioconda bioconductor-org.Mm.eg.db

mamba install -c r rstudio

Then start the conda-installed RStudio from within that environment:

rstudio

And the rest is business as usual. I haven't verified how stable this is or how it works in conjunction with other packages.
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0
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FYI, the deets of rstudio version

 rstudio                      1.1.456  h04f5b5a_1     r/osx-64
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