Entering edit mode
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.
I'm having the same problem and I wasn't able to solve it.
Hi, I am having the exact same problem. My system is old (Windows 7) but other than Bioconductor the rest is working just fine.