Question: Error: With R version 3.5 or greater, install Bioconductor packages using BiocManager
gravatar for Aki Hoji
24 days ago by
Aki Hoji10
Aki Hoji10 wrote:


Every update/installation of packages by BiocManager fails with a following typical error message;

*   Trying
* Connected to ( port 443 (#0)
* ALPN, offering http/1.1
* Cipher selection: ALL:!EXPORT:!EXPORT40:!EXPORT56:!aNULL:!LOW:!RC4:@STRENGTH
* successfully set certificate verify locations:
*   CAfile: /etc/ssl/cert.pem
  CApath: none
* SSL connection using TLSv1.2 / ECDHE-RSA-AES128-GCM-SHA256
* ALPN, server accepted to use http/1.1
* Server certificate:
*  subject: OU=Domain Control Validated; CN=*
*  start date: Oct  5 14:24:38 2016 GMT
*  expire date: Oct  3 18:30:38 2019 GMT
*  subjectAltName: host "" matched cert's ""
*  issuer: C=US; ST=Arizona; L=Scottsdale;, Inc.; OU=; CN=Go Daddy Secure Certificate Authority - G2
*  SSL certificate verify ok.
> GET /biocLite.R HTTP/1.1
User-Agent: libcurl/7.54.0
Accept: */*

< HTTP/1.1 200 OK
< Content-Length: 8355
< Connection: keep-alive
< Server: Apache/2.4.18 (Ubuntu)
< Last-Modified: Wed, 05 Jun 2019 12:00:02 GMT
< Accept-Ranges: bytes
< Date: Sun, 25 Aug 2019 14:05:11 GMT
< ETag: "20a3-58a925659f7b8"
< Cache-Control: max-age=60
< Age: 29
< X-Cache: Hit from cloudfront
< Via: 1.1 (CloudFront)
< X-Amz-Cf-Pop: ORD52-C2
< X-Amz-Cf-Id: w2fd4plWyxXXjT9rHPnZnvHb0dc7oOh4q-HRYvg3xKyzE1vWqWwSnQ==
* Connection #0 to host left intact
Error: With R version 3.5 or greater, install Bioconductor packages using BiocManager; see
Execution halted

If I use R --vanilla I don't run into this issue but otherwise (even in the absence of custom Makevars and .Rprofile), this happens constantly.

My system;

ProductName:    Mac OS X
ProductVersion: 10.14.6
BuildVersion:   18G87

R version (brew installed)

R: stable 3.6.1 (bottled)
Software environment for statistical computing
/usr/local/Cellar/R/3.6.1_1 (2,121 files, 56.8MB)
  Poured from bottle on 2019-08-24 at 08:33:00
==> Dependencies
Build: pkg-config ✔
Required: gcc ✔, gettext ✔, jpeg ✔, libpng ✔, openblas ✔, pcre ✔, readline ✔, xz ✔


> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin18.6.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /usr/local/Cellar/openblas/0.3.7/lib/libopenblasp-r0.3.7.dylib

Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 

[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] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocManager_1.30.4    edgeR_3.26.7          limma_3.40.6          Vennerable_3.1.0.9000

loaded via a namespace (and not attached):
 [1] enrichplot_1.4.0       bit64_0.9-7            RColorBrewer_1.1-2     progress_1.2.2        
 [5] httr_1.4.1             UpSetR_1.4.0           tools_3.6.1            backports_1.1.4       
 [9] R6_2.4.0               plotROC_2.2.1          DBI_1.0.0              lazyeval_0.2.2        
[13] BiocGenerics_0.30.0    colorspace_1.4-1       tidyselect_0.2.5       gridExtra_2.3         
[17] prettyunits_1.0.2      bit_1.1-14             compiler_3.6.1         graph_1.62.0          
[21] Biobase_2.44.0         xml2_1.2.1             triebeard_0.3.0        scales_1.0.0          
[25] ggridges_0.5.1         RBGL_1.60.0            stringr_1.4.0          digest_0.6.20         
[29] DOSE_3.10.2            pkgconfig_2.0.2        rlang_0.4.0            rstudioapi_0.10       
[33] RSQLite_2.1.2          gridGraphics_0.4-1     farver_1.1.0           jsonlite_1.6          
[37] BiocParallel_1.18.1    GOSemSim_2.10.0        dplyr_0.8.3            magrittr_1.5          
[41] ggplotify_0.0.4        GO.db_3.8.2            Matrix_1.2-17          Rcpp_1.0.2            
[45] munsell_0.5.0          S4Vectors_0.22.0       viridis_0.5.1          yaml_2.2.0            
[49] stringi_1.4.3          ggraph_1.0.2           MASS_7.3-51.4          plyr_1.8.4            
[53] qvalue_2.16.0          grid_3.6.1             blob_1.2.0             parallel_3.6.1        
[57] ggrepel_0.8.1          DO.db_2.9              crayon_1.3.4           lattice_0.20-38       
[61] cowplot_1.0.0          splines_3.6.1          hms_0.5.1              locfit_1.5-9.1        
[65] zeallot_0.1.0          pillar_1.4.2           fgsea_1.10.1           igraph_1.2.4.1        
[69] ggpubr_0.2.2           ggsignif_0.6.0         reshape2_1.4.3         stats4_3.6.1          
[73] fastmatch_1.1-0        glue_1.3.1             data.table_1.12.2      vctrs_0.2.0           
[77] tweenr_1.0.1           urltools_1.7.3         gtable_0.3.0           purrr_0.3.2           
[81] polyclip_1.10-0        tidyr_0.8.3            assertthat_0.2.1       ggplot2_3.2.1         
[85] ggforce_0.3.1          europepmc_0.3          viridisLite_0.3.0      tibble_2.1.3          
[89] clusterProfiler_3.12.0 rvcheck_0.1.3          AnnotationDbi_1.46.1   memoise_1.1.0         
[93] IRanges_2.18.2

Any pointers to fix this issue will be appreciated.

software error • 154 views
ADD COMMENTlink modified 23 days ago • written 24 days ago by Aki Hoji10

Well, if you are using "source("") or biocLite()" to install packages ignore it and instead use the BiocManager::install() command.

Also, if you updated R but still using the same library of packages that were installed when running R (ex. R3.5) , try to update newer version of Bioconductor.:

BiocManager::install(version = "3.10")
ADD REPLYlink written 24 days ago by shahryary30
Answer: Error: With R version 3.5 or greater, install Bioconductor packages using BiocMa
gravatar for Martin Morgan
24 days ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:

I read your post to say that you have no problems with R --vanilla, but do if starting with plain R.

The ?Startup help page describes which files are referenced when R starts up, and also which files --vanilla causes R to skip. Review the files (e.g., start R --vanilla and source() each file that exists) to identify the (non-default) content that triggers the verbose output during download.

ADD COMMENTlink written 24 days ago by Martin Morgan ♦♦ 23k
Answer: Error: With R version 3.5 or greater, install Bioconductor packages using BiocMa
gravatar for Aki Hoji
23 days ago by
Aki Hoji10
Aki Hoji10 wrote:

I found a culprit. I have three R project directories and home directory and each of those have .Rprofile. I thought I commented out/deleted "source("") from all the .Rprofile but I missed removing it from one of them. Now the problem solved. Thanks @shahryary and Martin Morgan for suggestions.

ADD COMMENTlink written 23 days ago by Aki Hoji10
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 297 users visited in the last hour