Closed lidanwu closed 2 years ago
It's possible this is a one-off server error.
@patrickjdanaher, I encountered a different error when running big dataset with insitutype()
and there's session error message before the error associated with insitutype()
. It seems like the current insitutype()
is not working on dataset of 80k cells.
The script I ran after finding anchor cells using find_anchor_cells()
:
semiSupRes <- insitutype(counts = Matrix::t(Giotto:::get_expression_values(gem, 'rna', 'raw')),
neg = Matrix::rowMeans(Matrix::t(Giotto:::get_expression_values(gem, 'negprobes', 'raw'))),
init_clust = NULL,
n_clusts = config_nbclust$n_clusts,
fixed_profiles = refProfiles,
anchors = anchors)
error message showed up at step:
log and error message in console:
clustering all cells
phase 1: random starts in 5000 cell subsets
17.7 cells per geometric bin.
17.7 cells per geometric bin.
17.7 cells per geometric bin.
2022-04-05T19:40:18.536393Z [rsession-rstudio] ERROR offlineConnectionMatcher: ignoring connection received in the future; LOGGED FROM: bool rstudio::session::offlineConnectionMatcher(rstudio_boost::shared_ptr<rstudio::session::HttpConnection>, std::chrono::_V2::steady_clock::time_point) src/cpp/session/SessionOfflineService.cpp:130
2022-04-05T19:40:18.536438Z [rsession-rstudio] ERROR offlineConnectionMatcher: ignoring connection received in the future; LOGGED FROM: bool rstudio::session::offlineConnectionMatcher(rstudio_boost::shared_ptr<rstudio::session::HttpConnection>, std::chrono::_V2::steady_clock::time_point) src/cpp/session/SessionOfflineService.cpp:130
2022-04-05T19:40:18.536448Z [rsession-rstudio] ERROR offlineConnectionMatcher: ignoring connection received in the future; LOGGED FROM: bool rstudio::session::offlineConnectionMatcher(rstudio_boost::shared_ptr<rstudio::session::HttpConnection>, std::chrono::_V2::steady_clock::time_point) src/cpp/session/SessionOfflineService.cpp:130
2022-04-05T19:40:20.499245Z [rsession-rstudio] ERROR R.getOption: rstudio.errors.suppressed made from non-main thread; LOGGED FROM: SEXPREC* rstudio::r::options::getOption(const string&) src/cpp/r/ROptions.cpp:83
2022-04-05T19:40:20.499416Z [rsession-rstudio] ERROR evaluateExpression called from thread other than main; LOGGED FROM: rstudio::core::Error rstudio::r::exec::{anonymous}::evaluateExpressionsUnsafe(SEXP, SEXP, SEXPREC**, rstudio::r::sexp::Protect*, rstudio::r::exec::{anonymous}::EvalType) src/cpp/r/RExec.cpp:140
2022-04-05T19:40:20.499524Z [rsession-rstudio] ERROR R.getOption: rstudio.errors.suppressed made from non-main thread; LOGGED FROM: SEXPREC* rstudio::r::options::getOption(const string&) src/cpp/r/ROptions.cpp:83
2022-04-05T19:40:20.499551Z [rsession-rstudio] ERROR evaluateExpression called from thread other than main; LOGGED FROM: rstudio::core::Error rstudio::r::exec::{anonymous}::evaluateExpressionsUnsafe(SEXP, SEXP, SEXPREC**, rstudio::r::sexp::Protect*, rstudio::r::exec::{anonymous}::EvalType) src/cpp/r/RExec.cpp:140
2022-04-05T19:40:20.722376Z [rsession-rstudio] ERROR R.getOption: rstudio.errors.suppressed made from non-main thread; LOGGED FROM: SEXPREC* rstudio::r::options::getOption(const string&) src/cpp/r/ROptions.cpp:83
2022-04-05T19:40:20.722464Z [rsession-rstudio] ERROR evaluateExpression called from thread other than main; LOGGED FROM: rstudio::core::Error rstudio::r::exec::{anonymous}::evaluateExpressionsUnsafe(SEXP, SEXP, SEXPREC**, rstudio::r::sexp::Protect*, rstudio::r::exec::{anonymous}::EvalType) src/cpp/r/RExec.cpp:140
2022-04-05T19:40:20.922611Z [rsession-rstudio] ERROR R.getOption: rstudio.errors.suppressed made from non-main thread; LOGGED FROM: SEXPREC* rstudio::r::options::getOption(const string&) src/cpp/r/ROptions.cpp:83
2022-04-05T19:40:20.922674Z [rsession-rstudio] ERROR evaluateExpression called from thread other than main; LOGGED FROM: rstudio::core::Error rstudio::r::exec::{anonymous}::evaluateExpressionsUnsafe(SEXP, SEXP, SEXPREC**, rstudio::r::sexp::Protect*, rstudio::r::exec::{anonymous}::EvalType) src/cpp/r/RExec.cpp:140
2022-04-05T19:40:21.122876Z [rsession-rstudio] ERROR R.getOption: rstudio.errors.suppressed made from non-main thread; LOGGED FROM: SEXPREC* rstudio::r::options::getOption(const string&) src/cpp/r/ROptions.cpp:83
2022-04-05T19:40:21.122946Z [rsession-rstudio] ERROR evaluateExpression called from thread other than main; LOGGED FROM: rstudio::core::Error rstudio::r::exec::{anonymous}::evaluateExpressionsUnsafe(SEXP, SEXP, SEXPREC**, rstudio::r::sexp::Protect*, rstudio::r::exec::{anonymous}::EvalType) src/cpp/r/RExec.cpp:140
2022-04-05T19:40:21.323157Z [rsession-rstudio] ERROR R.getOption: rstudio.errors.suppressed made from non-main thread; LOGGED FROM: SEXPREC* rstudio::r::options::getOption(const string&) src/cpp/r/ROptions.cpp:83
2022-04-05T19:40:21.323230Z [rsession-rstudio] ERROR evaluateExpression called from thread other than main; LOGGED FROM: rstudio::core::Error rstudio::r::exec::{anonymous}::evaluateExpressionsUnsafe(SEXP, SEXP, SEXPREC**, rstudio::r::sexp::Protect*, rstudio::r::exec::{anonymous}::EvalType) src/cpp/r/RExec.cpp:140
2022-04-05T19:40:21.523435Z [rsession-rstudio] ERROR R.getOption: rstudio.errors.suppressed made from non-main thread; LOGGED FROM: SEXPREC* rstudio::r::options::getOption(const string&) src/cpp/r/ROptions.cpp:83
2022-04-05T19:40:21.523497Z [rsession-rstudio] ERROR evaluateExpression called from thread other than main; LOGGED FROM: rstudio::core::Error rstudio::r::exec::{anonymous}::evaluateExpressionsUnsafe(SEXP, SEXP, SEXPREC**, rstudio::r::sexp::Protect*, rstudio::r::exec::{anonymous}::EvalType) src/cpp/r/RExec.cpp:140
2022-04-05T19:40:21.723708Z [rsession-rstudio] ERROR R.getOption: rstudio.errors.suppressed made from non-main thread; LOGGED FROM: SEXPREC* rstudio::r::options::getOption(const string&) src/cpp/r/ROptions.cpp:83
2022-04-05T19:40:21.723777Z [rsession-rstudio] ERROR evaluateExpression called from thread other than main; LOGGED FROM: rstudio::core::Error rstudio::r::exec::{anonymous}::evaluateExpressionsUnsafe(SEXP, SEXP, SEXPREC**, rstudio::r::sexp::Protect*, rstudio::r::exec::{anonymous}::EvalType) src/cpp/r/RExec.cpp:140
Error in FUN(newX[, i], ...) : '...' used in an incorrect context
2022-04-05T19:40:21.923985Z [rsession-rstudio] ERROR R.getOption: rstudio.errors.suppressed made from non-main thread; LOGGED FROM: SEXPREC* rstudio::r::options::getOption(const string&) src/cpp/r/ROptions.cpp:83
2022-04-05T19:40:21.924042Z [rsession-rstudio] ERROR evaluateExpression called from thread other than main; LOGGED FROM: rstudio::core::Error rstudio::r::exec::{anonymous}::evaluateExpressionsUnsafe(SEXP, SEXP, SEXPREC**, rstudio::r::sexp::Protect*, rstudio::r::exec::{anonymous}::EvalType) src/cpp/r/RExec.cpp:140
Called from: FUN(newX[, i], ...)
This might have failed because of a server error, or perhaps because it was sparse matrices, not matrices used.
Takeaway: insitutype should accept diverse matrix types.
Under the conclusion that this arose from the matrix type being input, closing this issue and opening a new one asking for the necessary fix.
I encountered an error when running
insitutype()
for supervised cell typing on dataset of single slide.Error message showed up after 10 random starts within phase 1, but It's uncler whether it happens on L203 or L216 of
runinstituetype()
: