Error: 'src_sql' is not an exported object from 'namespace:dplyr'

[lptolik]

Hi,

I've recently updated version of the dplyr package and got the following error:

library(DBI) library(dplyr) library(MonetDBLite) dbdir <- '~/path/to/db/dir/' prepareCon<-function(dbdir){ con <- dbConnect(MonetDBLite::MonetDBLite(), dbdir) if(dbIsValid(con)){ cat(paste(dbGetInfo(con),collapse = '\n')) }else{ stop('DB is not connected') } dbBegin(con) return(con) } con <- prepareCon(dbdir) monetdb_conn <- src_monetdb(con = con)

The last statement returns an error:

Error: 'src_sql' is not an exported object from 'namespace:dplyr'

The connection is working fine, the problem is in dplyr association.

Recent dplyr documentation proposed to call dplyr::tbl with connection:

t<- tbl(con,'spectra') Error in dbFetch(qry, 0) : Fetch 0 rows? Really?

That does not work as well. The code was functional with dplyr 0.5, on their site they listed that type of errors and send to your bugtracker.

[ajdamico]

hi, could you double-check this with the development version? i cannot reproduce these errors

devtools::install_github("hannesmuehleisen/MonetDBLite")

[lptolik]

devtools::install_github("hannesmuehleisen/MonetDBLite") Downloading GitHub repo hannesmuehleisen/MonetDBLite@master from URL https://api.github.com/repos/hannesmuehleisen/MonetDBLite/zipball/master Installation failed: Could not find build tools necessary to build MonetDBLite

CRAN version installed properly.

[ajdamico]

hi, that sounds like a separate issue. please do some googling to fix. maybe this? thanks

https://github.com/hadley/devtools/issues/1176#issuecomment-217750428

[lptolik]

Hi, I'm on MacOS:

R version 3.3.2 (2016-10-31) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: macOS Sierra 10.12.5

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] stats graphics grDevices utils datasets methods base

other attached packages: [1] MonetDBLite_0.3.1

loaded via a namespace (and not attached): [1] httr_1.2.1 R6_2.2.2 DBI_0.7 tools_3.3.2 withr_1.0.2 curl_2.7 memoise_1.1.0 codetools_0.2-15 [9] git2r_0.18.0 digest_0.6.12 devtools_1.13.2

[ajdamico]

i do not think your issue is related to monetdblite? did you upgrade gcc?

[hannes]

I think you need to install Xcode command line tools

On 5 Jul 2017, at 19:47, Anthony Damico notifications@github.com wrote:

i do not think your issue is related to monetdblite? did you upgrade gcc?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

[lptolik]

yes, I've updated clang, gcc, installed R 3.4 and now I have a problem with shared library:

devtools::install_github("hannesmuehleisen/MonetDBLite") Downloading GitHub repo hannesmuehleisen/MonetDBLite@master from URL https://api.github.com/repos/hannesmuehleisen/MonetDBLite/zipball/master Installing MonetDBLite '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ \ --no-save --no-restore --quiet CMD INSTALL \ '/private/var/folders/b2/vx2cstxj6kd4_0tc428h4_qm0000gn/T/RtmpCcWTc9/devtools7c852406336e/hannesmuehleisen-MonetDBLite-3cb70b3' \ --library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library' \ --install-tests

• installing source package ‘MonetDBLite’ ... configure: creating cache config.cache checking build system type... x86_64-apple-darwin16.6.0 checking host system type... x86_64-apple-darwin16.6.0 checking target system type... x86_64-apple-darwin16.6.0 checking for a BSD-compatible install... /usr/local/bin/ginstall -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/local/bin/gmkdir -p checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether UID '501' is supported by ustar format... yes checking whether GID '20' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking for pkg-config... /usr/local/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for style of include used by make... GNU checking for gcc... /usr/local/opt/llvm/bin/clang -fopenmp checking whether the C compiler works... no configure: error: in /private/var/folders/b2/vx2cstxj6kd4_0tc428h4_qm0000gn/T/RtmpCcWTc9/devtools7c852406336e/hannesmuehleisen-MonetDBLite-3cb70b3/src': configure: error: C compiler cannot create executables Seeconfig.log' for more details rm: libmonetdb5.so: No such file or directory libs arch - /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB -lz -o libmonetdb5.so find -name "*.o" | xargs echo R tests preparing package for lazy loading help * installing help indices building package indices ** testing if installed package can be loaded Error: package or namespace load failed for ‘MonetDBLite’ in library.dynam(lib, package, package.lib): shared object ‘libmonetdb5.so’ not found Error: loading failed Execution halted ERROR: loading failed
• removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/MonetDBLite’
• restoring previous ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/MonetDBLite’ Installation failed: Command failed (1)

I have reinstall monetdb via Homebrew, but I don't have libmonetdb5.so, I have libmonetdb5.dylib

[hannes]

" C compiler cannot create executables " that's the issue here I think.

[lptolik]

Hi, I've manage to compile, the problem was in OpenMP support in clang4 for Mac. The error disappeared with version from github, but a can confirm, that the error exists on CRAN binary version for Mac and Windows.

Cheers, Anatoly

[ajdamico]

makes sense since there was a big dplyr update recently and the monetdblite cran version is a year old. i think hannes plans to release the github version to cran in the next month. thanks for following up!