Tmp Dir Error
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I am using R v. 3.5.2 on Windows and when performing the "qza_to_phyloseq" command Error in unzip(file, exdir = tmp) : 'exdir' does not exist.
I tried setting tmp to an empty folder in my working directory as I saw on other threads but end up with another error of Error in file(con, "r") : cannot open the connection.
I know that my working directory is set correctly and that the file names are all correct.
Does this problem also happen when using read_qza to read a single artifact?
Does this problem also happen when using read_qza to read a single artifact?
Nope that's what is so confusing! I am able to successfully import all of my files to my R studio workspace using the commands in one of your tutorials. For example:
SVs=read_qza("secchi-daily-table.qza")
Ahhh, i see what the issue was. It should be fixed now!
Ahhh, i see what the issue was. It should be fixed now!
I still am getting the same "cannot open the connection" error
Did you reinstall from github using devtools::install_github("jbisanz/qiime2R") ?
Sadly, yes. I am wondering if maybe this is potentially an issue with my computer? What do you think?
Can you post exactly the command you are using and the results of sessionInfo()?
The exact commands I have tried:
phy=qza_to_phyloseq("daily-table.qza", "daily-rooted-tree.qza","daily-tax.qza", "daily_meta_cat.tsv")
phy=qza_to_phyloseq("daily-table.qza", "daily-rooted-tree.qza","daily-tax.qza", "daily_meta_cat.tsv", tmp="test")
For the second one the tmp is just set to an empty folder in my working directory. Both give the same connection error. I have also double checked that my working directory is still set up properly and it appears to be.
I tried updating my R to 3.6 as well just to try that out...so this is the session info with the 3.6 update:
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
Matrix products: default
Random number generation:
RNG: Mersenne-Twister
Normal: Inversion
Sample: Rounding
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] Biostrings_2.52.0 XVector_0.24.0 IRanges_2.18.1 S4Vectors_0.22.0 BiocGenerics_0.30.0
[6] biomformat_1.12.0 BiocManager_1.30.4 yaml_2.2.0 Hmisc_4.2-0 ggplot2_3.2.0
[11] Formula_1.2-3 survival_2.44-1.1 lattice_0.20-38 qiime2R_0.99.12 phyloseq_1.27.6
loaded via a namespace (and not attached):
[1] Rcpp_1.0.1 ape_5.3 assertthat_0.2.1 digest_0.6.20 foreach_1.4.4
[6] R6_2.4.0 plyr_1.8.4 backports_1.1.4 acepack_1.4.1 pillar_1.4.2
[11] zlibbioc_1.30.0 rlang_0.4.0 lazyeval_0.2.2 rstudioapi_0.10 data.table_1.12.2
[16] vegan_2.5-5 rpart_4.1-15 Matrix_1.2-17 checkmate_1.9.4 splines_3.6.1
[21] stringr_1.4.0 foreign_0.8-71 htmlwidgets_1.3 igraph_1.2.4.1 munsell_0.5.0
[26] compiler_3.6.1 xfun_0.8 pkgconfig_2.0.2 base64enc_0.1-3 multtest_2.40.0
[31] mgcv_1.8-28 htmltools_0.3.6 nnet_7.3-12 tidyselect_0.2.5 tibble_2.1.3
[36] gridExtra_2.3 htmlTable_1.13.1 codetools_0.2-16 permute_0.9-5 withr_2.1.2
[41] crayon_1.3.4 dplyr_0.8.3 MASS_7.3-51.4 grid_3.6.1 nlme_3.1-140
[46] jsonlite_1.6 gtable_0.3.0 magrittr_1.5 scales_1.0.0 stringi_1.4.3
[51] reshape2_1.4.3 latticeExtra_0.6-28 Rhdf5lib_1.6.0 RColorBrewer_1.1-2 iterators_1.0.10
[56] tools_3.6.1 ade4_1.7-13 Biobase_2.44.0 glue_1.3.1 purrr_0.3.2
[61] colorspace_1.4-1 rhdf5_2.28.0 cluster_2.1.0 knitr_1.23
We have solved the issue. It was a hidden file extension and now it's working great.