Bioconductor version cannot be validated
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xlu.cpu • 0
@xlucpu-24099
Last seen 7 months ago
France

Hi, I am not able to download any package from Bioconductor. For example,

BiocManager::install("ACE")

Error: Bioconductor version cannot be validated; no internet connection?  See #troubleshooting section in vignette
In addition: Warning messages:
1: In file(con, "r") :
  URL 'https://bioconductor.org/config.yaml': status was 'SSL connect error'
2: In readLines(...) : line 6 appears to contain an embedded nul
3: In readLines(...) :
  incomplete final line found on 'http://bioconductor.org/config.yaml'

I am able to assess any website instead of https://bioconductor.org/config.yaml. I have tried many alternatives listed online, for example:

options(download.file.method = 'libcurl')
options(url.method = 'libcurl')

or

options(BioC_mirror = "http://bioconductor.org")

options(
  BIOCONDUCTOR_ONLINE_VERSION_DIAGNOSIS = FALSE
)

options(
  BIOCONDUCTOR_CONFIG_FILE = "D:/system/Desktop/bioconductor.org_config.yaml"
)

None of them worked!

This is my session info:

> sessionInfo()
R version 4.2.2 (2022-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8  LC_CTYPE=Chinese (Simplified)_China.utf8    LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                                LC_TIME=Chinese (Simplified)_China.utf8    

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

other attached packages:
[1] Biobase_2.58.0      BiocGenerics_0.44.0

loaded via a namespace (and not attached):
  [1] utf8_1.2.2                  tidyselect_1.2.0            RSQLite_2.2.18              AnnotationDbi_1.60.0        grid_4.2.2                 
  [6] BiocParallel_1.32.1         munsell_0.5.0               ScaledMatrix_1.6.0          codetools_0.2-18            preprocessCore_1.60.0      
 [11] nleqslv_3.3.3               withr_2.5.0                 colorspace_2.0-3            filelock_1.0.2              knitr_1.40                 
 [16] leaps_3.1                   rstudioapi_0.14             stats4_4.2.2                SingleCellExperiment_1.20.0 robustbase_0.95-0          
 [21] ggsignif_0.6.4              NMF_0.24.0                  MatrixGenerics_1.10.0       GenomeInfoDbData_1.2.9      KMsurv_0.1-5               
 [26] bit64_4.0.5                 pheatmap_1.0.12             rhdf5_2.42.0                vctrs_0.5.0                 generics_0.1.3             
 [31] xfun_0.34                   BiocFileCache_2.6.0         R6_2.5.1                    doParallel_1.0.17           GenomeInfoDb_1.34.9        
 [36] illuminaio_0.40.0           rsvd_1.0.5                  locfit_1.5-9.6              bitops_1.0-7                rhdf5filters_1.10.0        
 [41] cachem_1.0.6                reshape_0.8.9               DelayedArray_0.23.2         assertthat_0.2.1            BiocIO_1.8.0               
 [46] scales_1.2.1                gtable_0.3.1                beachmat_2.14.0             affy_1.76.0                 methylumi_2.44.0           
 [51] lsr_0.5.2                   rlang_1.1.1                 genefilter_1.80.0           splines_4.2.2               rtracklayer_1.58.0         
 [56] rstatix_0.7.1               impute_1.72.0               GEOquery_2.66.0             inline_0.3.19               broom_1.0.1                
 [61] BiocManager_1.30.22         yaml_2.3.6                  reshape2_1.4.4              abind_1.4-5                 GenomicFeatures_1.50.2     
 [66] backports_1.4.1             tools_4.2.2                 gridBase_0.4-7              nor1mix_1.3-0               ggplot2_3.4.2              
 [71] affyio_1.68.0               ellipsis_0.3.2              lumi_2.50.0                 RColorBrewer_1.1-3          DNAcopy_1.72.0             
 [76] siggenes_1.72.0             Rcpp_1.0.9                  plyr_1.8.8                  sparseMatrixStats_1.10.0    ROC_1.74.0                 
 [81] progress_1.2.2              zlibbioc_1.44.0             purrr_1.0.1                 RCurl_1.98-1.9              prettyunits_1.1.1          
 [86] ggpubr_0.4.0                openssl_2.0.4               bumphunter_1.40.0           zoo_1.8-11                  S4Vectors_0.36.0           
 [91] SummarizedExperiment_1.28.0 cluster_2.1.4               magrittr_2.0.3              data.table_1.14.4           survminer_0.4.9            
 [96] mvtnorm_1.1-3               wateRmelon_2.4.0            matrixStats_0.62.0          hms_1.1.2                   GSVA_1.46.0                
[101] xtable_1.8-4                XML_3.99-0.12               BMA_3.18.17                 mclust_6.0.0                gridExtra_2.3              
[106] IRanges_2.32.0              compiler_4.2.2              biomaRt_2.54.1              minfi_1.44.0                tibble_3.1.8               
[111] KernSmooth_2.23-20          crayon_1.5.2                pcaPP_2.0-3                 mgcv_1.8-41                 tzdb_0.3.0                 
[116] rrcov_1.7-2                 tidyr_1.2.1                 geneplotter_1.76.0          DBI_1.1.3                   clustvarsel_2.3.4          
[121] dbplyr_2.3.0                MASS_7.3-58.1               rappdirs_0.3.3              Matrix_1.5-3                car_3.1-1                  
[126] readr_2.1.3                 cli_3.4.1                   survtype_1.14.0             quadprog_1.5-8              parallel_4.2.2             
[131] km.ci_0.5-6                 GenomicRanges_1.49.0        pkgconfig_2.0.3             GenomicAlignments_1.34.0    registry_0.5-1             
[136] xml2_1.3.3                  foreach_1.5.2               annotate_1.76.0             rngtools_1.5.2              pkgmaker_0.32.2            
[141] multtest_2.54.0             beanplot_1.3.1              XVector_0.38.0              maftools_2.14.0             doRNG_1.8.2                
[146] scrime_1.3.5                stringr_1.4.1               digest_0.6.30               graph_1.76.0                Biostrings_2.66.0          
[151] base64_2.0.1                survMisc_0.5.6              DelayedMatrixStats_1.20.0   GSEABase_1.60.0             restfulr_0.0.15            
[156] curl_4.3.3                  Rsamtools_2.14.0            rjson_0.2.21                lifecycle_1.0.3             nlme_3.1-160               
[161] Rhdf5lib_1.20.0             carData_3.0-5               viridisLite_0.4.1           askpass_1.1                 limma_3.54.0               
[166] BSgenome_1.66.3             fansi_1.0.3                 pillar_1.8.1                lattice_0.20-45             DEoptimR_1.0-11            
[171] KEGGREST_1.38.0             fastmap_1.1.0               httr_1.4.4                  survival_3.4-0              glue_1.6.2                 
[176] png_0.1-7                   iterators_1.0.14            bit_4.0.4                   stringi_1.7.8               HDF5Array_1.26.0           
[181] blob_1.2.3                  DESeq2_1.38.0               BiocSingular_1.14.0         memoise_2.0.1               dplyr_1.0.10               
[186] irlba_2.3.5.1

Please help me, I am not able to run my program as it needs SSL connection.

Bioconductor • 1.1k views
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I'm having the same problem and I wasn't able to solve it.

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Hi, I am having the exact same problem. My system is old (Windows 7) but other than Bioconductor the rest is working just fine.

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